I love Scrivener but this program seems to be more geared toward prose and fiction writing. I will probably go back to Word for my academics. I just cannot figure out a good way to include citations in my text and collect them for the bibliography like word does. I use APA, Chicago, and MLM but don’t see how to do this in scrivener. Does anybody else has the same problem and how do you do it? Thanks for any advice, Michael
No problem.
I use Papers3 for my references, enter cite keys, export to Word when I am done and create the reference list.
There of lots of very productive academic users of Scrivener! I use Bookends (my own writing) and Endnote (if a collaborator forces me to), and use unformatted citations. Then generate the bibliography when you are finished[1].
CiteWYW (if you use Endnote) is quite fragile and an utter PITA when collaborating, and that is the only thing I can think is what you think Word can do? But you really don’t need CWYW to cite and generate bibliographies.
On the Mac at least ⌘Y quickly switches to my reference manager, and tap it again and I’m back in Scrivener. I also use Quicksilver (a customisable power launcher) to launch reference searches in Pubmed directly. So I can select a word in Scrivener and launch a Pubmed search or reference search in Bookends.
[1] I use Multimarkdown for all my compile requirements, and can scan the plain text before conversion to LibreOffice / Word, or just use Bookends/Endnote after opening the final format file. For real geeks, Pandoc can also automagically format citations from markdown.
As the OP is on Windows, Bookends, and I think Papers are no-go, being Mac only. That leaves him with Endnote—as he is doing a PhD, a licence may be available through his university—and Zotero, and some form of bibdesk, I presume.
But the principles are basically the same.
Mark
The OP could make the sensible switch to Mac, which would give more opportunities. 
I may be a very long-time Mac user myself, but I wouldn’t have the temerity to suggest that! 
Mark
I am a looong time Windows user (Win 1.0) and MS-DOS before that but made the switch a few years ago, although I do still have two Windows computers that I use sometimes, but not for serious work.
Maybe that’s a better way to phrase it then. “Maybe the OP should switch” with a smiley perhaps comes off a bit less fun than you intended (especially when using loaded words like “sensibly” in there which make judgements and undercut/distort the intended humor value).
I, for one, have a very hard time seeing any humor in the inevitable “switch to a Mac” crap that folks throw around in the Windows forum. If they don’t like Windows, don’t read the forum. It’s not helpful. Some of us do own Macs and we don’t use them for one reason or another, reasons that are valid for us. Whether or not the intent is to make a joke or not, the weight of all those comments is there and for some readers, it may create a hostile environment – one that you (the impersonal you) didn’t intend to tap into, but nevertheless you did because you can’t control perception.
“I was in a situation much the same, and for me what ended up being the right choice was to start using a Mac because of X, Y, and Z and here’s the benefit I received” takes that judgement factor away. You’re sharing what worked for you and inviting the reader to consider the thought experiment of whether it would work for them.
I use Endnote for referencing (mostly because I got it cheap when I was a graduate student and have been using it for so long that it’s second nature; I imagine that Zotero, Mendeley, etc. would all be just as good). I have never used the “cite while you write” feature in Word, mainly because I insert the Endnote references when I’m making notes, and I really don’t want them formatted or turned into bibliographies, etc. at this stage. But also because those notes get cut and pasted into numerous different documents over the years that I work on a topic, and I don’t know if/where they will be published until fairly late in the writing process, which is when I do the formatting.
So, adjusting to writing in Scrivener was very easy: as I’m making notes, I simply switch to Endnote (you can configure Scrivener so that its bibliographic shortcut will bring up your preferred citation manager, but I find it just as easy to Alt-Tab to the Endnote window); highlight the reference I want to use; copy it and then switch to Scrivener and paste it.
This gives me a temporary citation, which looks like this <Conn, 1900 #5095> (you can customise the kind of brackets you use; I use these <> for citations because I have always used their default ones {} for “notes to self”). You can add a reference to a page or range of pages to the citation like this <Conn, 1900 #5095@227–228>. Then as I make notes, I keep pasting the temporary citation and putting in the right page refs. For me, writing is mostly cutting and pasting from different sources, so the temporary citations all come along with the quotes, notes, etc.
Then I polish, amend, edit, etc. in Scrivener. Once I’m 99% happy, I compile the whole thing for Word and do the final formatting there, including using Endnote to transform all those temporary citations into final ones. I’m on my second book with Scrivener, and so far its working very well.
There are also ways to access EndNote and indicate the need for a citation and include citations.
Check the manual for instructions. (You can find it in the Help menu in the software.)