I am very glad to be able to highlight pdfs directly in Devonthink now. There seems to be a little issue, however. If I highlight something on line 15, say, and then go to highlight a word on line 16, say, the second highlighting knocks out the previous highlighting. Any thoughts?
That’s an artifact of the selection area. If the second line is close to the first, there can be overlap, the ‘space’ of the second line intruding into the ‘space’ of the first line.
Try this. Highlight a line in a PDF, then in a separate operation select part of the line immediately beneath it. Click and hold on ‘Format’ in the menu bar and inspect the ‘Highlight’ command. Is it already checked? If so, the highlighting of the first line will be erased if you click on the ‘Highlight’ command.
To verify that, repeat the highlighting test, but just select text in the second line. Now greatly magnify the view of the PDF and you will see an overlap of the selected area in the second line with the highlighting in the line above it.
As DEVONthink is using Apple’s PDFKit, I doubt that can be changed in DEVONthink.
I hadn’t noticed this because I’m probably a bit nutty. I treat my reference documents as though I’m the curator of a rare manuscript collection. Marking them up would be mutilation. 
I see. Skim must work on a different system, since I hadn’t noticed that issue.
As for keeping reference material clean of markup… well, you can unhighlight it too (as you know), which you can’t do with highlighter marker on paper.
Thanks,
Declan
I checked several other PDFs within a database and was able to highlight words under a previously highlighted line in several of them. It’s just a question of the spacing of the lines in a PDF.
I make a lot of notes and annotations when I’m working with references, but in one or more separate rich text notes, associated to the reference document by Name, links and perhaps searchable cue strings of text. I’ll often use a template RTF note in the Cornell Notes format, with links and cue strings in the left column and my comments, summaries and/or quotes in the right column. If I search for a document by name, my notes associated with it will show up as well. If I click on the Page Link to a PDF, the reference pops up, scrolled to the desired page. And of course my notes are all searchable.
As I’m nutty about avoiding marking up references, that saves the drudgery of making, then erasing markups. 
Bill, would you mind sharing that RTF template?
The one I’ve been using is just a little 2 row, 2 column table based on the Cornell Note layout (which you can see and download if you Google ‘Cornel Note’).
Eric has put together several new templates, including Cornell Note, with some attached scripting magic, to be included in public beta 7.