I drag pfd documents directly into scrivener. Is there a way I can highlight text or mark certain parts of the pdf. For example, can I click on a spot and add a note? Thanks! 
Use āOpen in external editorā. You can do this in three ways:
(1) through the menu Documents ā Open ā in external editor
(2) using the keyboard shortcut Ctrl-Cmd-O
(3) clicking the icon at the base of the PDf that looks like an āAā made with a ruler, a pencil and a paintbrush (press and hold if you want to choose what the PDF opens in).
Although a 3rd party app (most likely Appleās excellent Preview) will do the editing, the annotations will be visible if they use standard PDF methods (Skim, for example, doesnāt so I donāt think annotations made using it will show in Scrivener).
Though PDFPen isnāt my favorite app when it comes to syncing with itās iPad version, the notes made in it do carry over to Scrivener just fine.
Itās worth noting you can highlight text in Scrivener without an external editor, using the normal Shift-Cmd-H (Format/Highlight/Highlight Text). Itās just one colour though. For adding notes you do need external software.