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I haven't found a tool to do in-PDF annotation practically (pdfedit might be able to do it, but was never practical). Both Okular and Xournal can do annotation on top of PDFs, though. Okular includes text aware tools like yellow highlighter and black underlining, while Xournal is well adapted to pen use, with things like the shape recognizer. This of course doesn't mean the Pocketbook has similar features, but it means there are some source examples.
Both of those programs are built for full desktop environments which we don't have on the 903. They both use the same PDF engine as pdfviewer (poppler), and porting more is possible - but will take effort and time.
As pocketbook-free is a bit of a mixed bag, I haven't had the chance to test what's in pdfviewer there yet (didn't compile easily yet), and there may be in-house updates too, not to mention that Adobe viewer.
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