I believe you have to open the PDF in an external editor (Adobe Reader?) to highlight, but those highlights should show up in Scrivener once you save the pdf.
As for taking notes on note cards, here’s what I would do to stay organized:
Create a blank text document in the binder and “stack” it onto your pdf article. This will make the pdf file act as sort of a folder, in that it “contains” that blank document.
Select the PDF again and split the editor however you prefer (vertical or horizontal), and adjust things so you can read the pdf in one of the editors. Click into the OTHER, presumably smaller editor, and click the corkboard mode button (or use the View->Corkboard menu). Now you should see the pdf in one editor, and the new blank document stacked “in” or “under” it as an index card on a cork board.
Adjust the cork board using the tiny icons in the lower right of that editor’s footer bar to your preference.
Edit the title of that index card to include a very abbreviated version of the pdf’s article name, so you’ll always know at a glance what the source of your note was.
In the inspector, click the button at the bottom that looks like a few books on a shelf, and drag the pdf file from the binder to the reference pane in the inspector. This will make it so even if you move this note to somewhere else in the binder, you’ll be able to click on the reference to bring up the pdf from which you took your notes.
Now, back in the cork board, click once on the index card to highlight it, and hit CTRL-D (Documents->Duplicate in the menu) a few times to create a bunch of cards that will be titled for the article, and will have reference links to the pdf file.
Do this for every article you bring in to take notes from.
As you read the article in one editor, you can make notes on the next (mostly) blank index card, maybe adding the page number to the title, and then make your notes in the index card/synopsis area.
One last thing I recommend:
Go to View->Layout->Manage Layouts and save your editor split and corkboard settings via that interface. Whenever you want to return to this window arrangement, bring the Layouts window back up to choose your saved layout so that you don’t have to make all the window splits, resizing, and corkboard adjustments again.