Yes, you can do this too with Endnote — certainly if you were using Endnote from inside Word using their Word plug-in. But these possibilities take us rather afield from the issues at hand.
The important thing here, as I see it, is that the OP will not need to be “re-Compiling” her draft rtf output once the cite manager has processed it — nor will she need to tack her bibliography onto that manually.
Yep Already tried them, it was mendeley, zotero, and endnote were the ones they recommended. And my school doesn’t even know about scrivener- I found other school websites, like Cornell, that has some information. So now that I understand the general gist of it, I can probably work it through. Goal this week is to get this working on my grant proposal (small document) and continue practicing on the smaller stuff. Then when I actually start writing the thesis, I will hopefully have it down. Thanks for your advice. I’m going to post more questions on different topics that i’ve been messing around with like formatting, etc. Much appreciated.
@gr Very helpful explanation, thank you.
What field is your thesis in? There may be specialized solutions depending on the subject.
If you find yourself tearing your hair out trying to get things working. Then, rather than get a wig, you may want to consider shifting to a Mac. The extra cost will be compensated by stress relief. 
In any case you may also want to opt for an external monitor if you are working with a laptop just so that you can have a larger work space.
I am a Veterinarian and have been practicing emergency medicine for the past 15 years. I decided to go BACK to school ( I don’t suggest it- do it all at once, hehe) so that I can change positions within my field. So while practicing, I haven’t had to actually write any papers that required citations, etc. I am interested in infectious disease modeling and I may dabble in some AI. My hope is to detect foreign animal diseases early, to prevent massive economic loss to farms.
Except for the apple IIe back in the day, I’ve never had another apple anything (ipod, ipad, etc). I’ve built my previous computers so windows was always easier for me, and at some point, I plan on just switching to Linux entirely. I just need the time to figure it out. I already have my docking station and 2 extra monitors bc programming on a laptop is just not fun I have a surface pro 8 and love it for school. Way easier than carrying around 3 textbooks and 5 notebooks every day. hehe.
Even with all that, I actually have a hard time learning new software. I have a reading comprehension problem, so it just takes me longer to figure stuff out. Hardware - no problem. I love putting things together, but learning software is hard for me to understand. Just the way my brain works. So my PhD will be in Veterinary Epidemiology overall with a focus in modeling. So STEM field basically.
Why do people love Macs so much? Since most schools are windows based, I see allot of students having compatibility problems with some of the campus requirements so I just steered away from it. And most programmers lean towards Linux based systems.
They’re meant for the other ones. 
If you love tinkering with hardware, hunting for drivers, fighting viruses (and stopping the OS itself from spying on you), if you hate consistent user interfaces… in other words: If you enjoy your computer as a hobby, don’t get a Mac. It will just disappoint you in every possible way.
I started out with punch cards, then got a TRS Radioshack in 1979, then a series of CP/M and DRDOS based systems. Was with Microsoft based systems from 1986-2009. But when Microsoft was going to replace Windows XP with Vista I just couldn’t stand it anymore. That is when I seriously thought about Mac. I had friends who used Macs. I then read about how since Mac was now (no more) Intel based that VMs worked very well on them so that I could run XP or any other Windows version on them.
At first I was very reluctant, but the alternative of staying with Windows seemed worse, especially all the time I spent making sure my machine was not infected by something.
A friend of mine worked for Apple, at iTunes, and he got me my first MBP in 2009 at the employee discount (my wife still uses that machine) and I never looked back since then. I run Windows XP and Windows 10 in the VM if I need to do something with them. Windows runs better on the VM than it did native. And, I have never had to reinstall them.
I was pleasantly surprised at the variety and quality of the Mac based software a lot of which didn’t exist on Windows. Scrivener is an example of that, it was only later ported to Windows.
My programing days are long over and I am mostly interested in applications that further what I want to do rather than building applications.
I have thought about using Linux but it doesn’t support the software that I need for my work so no point going there.
On Macs the OS and hardware are a tight fit and just work. Significantly less problem with malware. It has excellent backup capabilities with Time Machine.
OS updates are frequent and free. Support is good.
The hardware is first class, all metal as opposed to all plastic. It is like a Mercedes compared to a Buick.
Other Mac users can give their own reasons. These are some of mine.
Brevity, the soul of wit.
Might just have to look into it for the future.
@November_Sierra - I actually do like building machines from the ground up. Can’t build your own Mac, so… but Orpheus’ points are well taken. I do see allot of engineers, graphics designers, etc with them. I would like to point out ’ don’t think for a second that apple is not ‘spying on you’. It totally is. Granted, Apple only collects about half the data that Google does per day, but it still does it.
By building my own, I can actually disable, and not even install allot of unnecessary Window’s ‘stuff’. And with proper computer ‘hygiene’ I call it, I haven’t had to worry about viruses etc in a long time.
Anyway, I know we digress on the original topic. Thank you guys for all your feedback. I appreciate the friendly conversation and your opinions. I will definitely be using them to try and work this out. I got two days before my proposal is due.
There’s nothing wrong with that, if you enjoy it. I used to build my own machines for a long time, I’ve worked in corporate environments which were dominated by Microsoft and proprietary niche business software, I was gaming. I thought that’s how you’re supposed to work with computers. Priorities change. Now I prefer calmness and peace of mind.
Yes you can. https://duckduckgo.com/?q=hakintosh&t=newext&atb=v274-1&ia=web
And then there is the new M1 and M2 chip-set that blows away Intel’s.
@Orpheus
Well I’ll be damned… I never even bothered to look anymore. That’s pretty cool. Will totally look into that in the future
And, be sure to look into the M series chipset. This is a vid that was made when it was introduced so it is a little dated, but you get the idea. https://www.youtube.com/watch?v=OuF9weSkS68
@Orpheus
Loved it! You don’t keep up with this stuff for a couple years and you fall way behind. Thanks for the new mindset. After this, no more school and then I can get back to my hobbies. Like building again.
on a different note, looked into JabRef. That seems like a good option, but I couldn’t find any videos on how to use it with scrivener. @nontroppo posts were helpful and suggested going from scrivener to pandoc (which I had to look up to see what that is) using JabRef. do you guys know of any how-to-video that can walk me through this process. I’m assuming I use the citekey to type into scrivener, then send it through to pandoc (which i’m still not sure I understand what that is), then have JabRef view that (I think this is where i’m mainly getting hung up).
Hi @Amalthya — I think you should probably steer clear of Pandoc for the moment. While Pandoc enables the “best” academic workflow from Scrivener and allows you to not need to do any scanning of RTF / ODT / DOCX files at all, it does require some software knowledge and familiarity with the command line, which I think you have stated is a distraction for you.
JabRef will work similarly to Zotero / Endnote, in that you enter temporary citations like \cite{derrien2022} when you write in Scrivener, then use a plugin for LibreOffice to create the Bibliography. The plugin can be downloaded here: GitHub - teertinker/JabRef_LibreOffice_Converter: A LibreOffice extension that converts JabRef references to plain text code and vice versa so that you can use your references with MS Office.
So here is my library in JabRef, note the Citationkey, that is the text that uniquely identifies each reference:
So we enter these citekeys into Scrivener like \cite{derrien2022}[1]. Now we compile from Scrivener to an ODT file, and you’ll see something like this in LibreOffice:
Press the highlighted icon for the plugin and it will convert those plain-text citations into JabRef “special” citations (they have grey shading):
Then in JabRef (after connecting to LibreOffice using the connect button), we use the ⟳ icon to [re]format the bibliography and citations:
Giving us:
One weakness of this workflow is that it doesn’t support footnotes, but this shouldn’t be an issue for science output.
I personally prefer LibreOffice, and I think Word doesn’t have a similar workflow with JabRef (it does have an integration but it uses the Word database that won’t allow using plain text intermediates I believe). So the question really is: what software do you want to use? I would use Endnote + Word or JabRef + LibreOffice. Zotero should support both but I don’t really remember that workflow now…
@nontroppo THANK YOU! That’s exactly what I needed. To be honest, it took me the last 4 hours to get it working, but I did. The cites are all messed up and not in the format I need, but I’ll just use the JabRef forums, etc to see how to format that in the program. I tested it out on a paragraph. JabRef doesn’t like webpages too much, hehe - I have to manually format the citationkey and looks like I’ll have to manually format the references as well. Didn’t put the webpage in the bibliography.
THANK YOU THANK YOU THANK YOU!!!
Yes, JabRef has some predefined styles for bibliographies here:
There is also a GUI to make new styles:
JabRef’s style language is not as advanced as CSL which is what Pandoc and Zotero use. But you now have a workflow that can be adapted in the future, and I think the JabRef forums should be able to help with these styles to get the formatting you desire…
One small trick is to use character styles in Scrivener to mark citations, then the compiler can add the \cite{ and } for you. Now if you change to pandoc you can use a different style rule and make [@citekey] pandoc citations without changing your source text at all 
I attach a scrivener project that does this, it uses a citation style so you only see the key in the text:
The compiler format has a style rule that adds \cite{ as a prefix and } as a suffix so you can compile to ODT.
LibreOfficeCite.scriv.zip (57.2 KB)
@nontroppo
found the styles, installed. I’m trying to get on the JabRef forums, but for some reason, i’m not getting the activation email, so contacted them for help. It previews fine in the entry editor, but when it exports the bibliography, it doesn’t look like the preview window. Still messing with it.
I appreciate all your help. Thanks for sticking with me.
If you need help with the jstyle file I can make one fairly easily. What format do you want your citations and bibliography entries to look like? I prefer author-year and always show the DOI and URL:
(Weber et al., 1988)
Weber, Max C., Simmel, Georg & Star, Susan (1988): Economy and Society. Journal of Sociology pp.45-69 (36). <http://wilkef.12hp.de> <http://dx.doi.org/10.1110\>
JStyle file:
NAME
General Author-Year with DOIs & URLs
PROPERTIES
Title="Bibliography"
IsSortByPosition=false
IsNumberEntries=false
ReferenceParagraphFormat="Standard"
ReferenceHeaderParagraphFormat="Standard"
CITATION
MaxAuthors=2
MaxAuthorsFirst=2
AuthorSeparator=", "
AuthorLastSeparator=" & "
EtAlString=" et al."
ItalicEtAl="true"
CitationSeparator="; "
MultiCiteChronological=true
BracketBefore="("
BracketAfter=")"
BracketBeforeInList="["
BracketAfterInList="]"
MinimumGroupingCount=3
CitationCharacterFormat="Standard"
FormatCitations=true
GroupedNumbersSeparator="-"
UniquefierSeparator=","
InTextYearSeparator=" "
YearSeparator=" "
LAYOUT
default=\begin{author}\format[Authors(LastFirst,Fullname,sep=\, ,LastSep= & ,EtAl= et al.,inf,9),]{\author} \end{author}\begin{year}(\year\uniq): \end{year}\begin{title}\format[RemoveLatexCommands]{\title}. \end{title}in: \begin{journal}\format[RemoveLatexCommands]{\journal} \end{journal}\begin{volume}(\format[RemoveLatexCommands]{\volume}).\end{volume}\begin{URL} <\URL\format[RemoveLatexCommands]{\empty}> \end{URL}<br>