Is there a way to “bookmark” within a large PDF document? Possibly some kind of linking strategy to various positions within the document. Also, I’m guessing there is no way to highlight or add a comment to a PDF while viewing. These would be great features for reading documents, as well as editing.
Christian has hinted that some of those features may come in a future version.
Even in the soon-to-be-released DT Pro 1.1, if the PDF has been captured using Index, or has been Imported to the database files folder, you will be able to open the PDF under Preview or Acrobat and add annotations, which will be reflected in the DT Pro database. You would still need Acrobat Pro to add really comprehensive bookmarks, but Preview will let you add searchable annotations (under OS X 10.4.4 or greater). In DT 1.1 just launch a PDF under Preview, edit it and save the changes. Select that PDF in DT Pro and you will see the edit changes via one-way synchronization from the edited file to the DT Pro display of the item.
DT Pro 1.1 and DT Personal 1.9.7 coming soon as free updates. Watch for the announcement.