Hey,
I am using the split screen feature of scrivener a lot, mainly to view a PDF that contains an assignment I am doing or something like that. What I really miss, are some tools to underline, mark, and comment stuff in the PDF (the yellow marker is not sufficient for me). Right now I have to add the annotations with Skim before importing the document into scrivener, and I really hate using two different programs for one task.
There wouldn’t need to be many more tools. Just underlining, new colours for the marker, comments and maybe a free-hand-drawing thing.
Would be nice! 
We use Apple’s PDF viewer, which as you note is somewhat simplistic, and it’s also a bit of a black box. We ask the Mac to display a provided PDF, and it returns are result that we print in the window. That’s pretty much it. There are a few access points which is how we got overstrike and highlight support in there, it’s how we can tell it to flip pages and change the view mode from single-page to two-page—but it’s impossible to add anything that isn’t already provided by it.
No need for Skim (as good as it is). You can do all the above (and more) in Preview which you can access from within Scrivener by either clicking on the Open in external editor icon (bottom right of the PDF display window), choosing Socuments → Open → in External Editor from the menu, or pressing Ctrl-Cmd-O.
I used to Skim for annotating PDFs, but then Preview caught up. I now use Preview for (almost) all of my PDF annotations. It does highlighting (in multiple colours), underlining, strikethrough, boxes, circles, lines, text (plain, speech bubble, thought bubble) or notes. Oh, plus adding signatures (kinda cool the way it uses the built-in camera to do that).
It’s not quite as good as being be to do ti within Scrivener, but you don’t need to edit before adding a PDF to Scrivener as it is a simple keyboard shortcut to open any PDF in Preview.
Note: if you really want to continue using Skim, you can do that too. I’m just not sure if you can set a keyboard shortcut.
Yes, you can use Skim as an external PDF editor just as well. There would be two ways of going about it. By default the Mac sets up Preview to view PDFs, but you can choose any PDF viewer you prefer by changing the default viewer with Finder. That all by itself will make Scrivener (and any other program that initiates file loads through the system) to use Skim. All the shortcut does in Scrivener is trigger a default system file load. On your computer, it is still Preview. On mine it is Skim.
The other way is to change Scrivener’s default so that it contradicts the system default. You can do that by using the application button in the footer bar. Instead of clicking it (the same as Ctrl-Cmd-O), right-click it, and select which application to load the PDF in. The text of the resulting dialogue box will explain how that feature works.
The overall list of precedence for what happens when you click the load externally button (or press the shortcut) is:
- Scrivener’s per-file override.
- Scrivener’s file-type override.
- The individual file’s Finder override (set with Get Info).
- The Finder’s file-type default.
If all you want to do is load all PDF’s in Skim, then, the best solution is to change Finder’s file-type default with the “Change All…” button in Get Info.
Incidentally you can use Skim to edit PDFs that have been imported into Scrivener. Just make sure to use Export to save it, with embedded notes, rather than the default. Skim’s default annotation model doesn’t use the PDF standard for saving annotations. Unfortunately it cannot edit embedded annotations (which is why this isn’t a default, I’m sure). Preview does win on that score, but I do still like Skim’s overall UI better.