Marking selected text in PDF open in Web Viewer on Mac

I just wondered whether any of you have any solution (or know about it) whereby PDF files in the 'web viewer' can be marked using the Acrobat reader Pro (I use version 9) . I use Mac platform., FMP Pro advance11 (switching to 13 soon). Marking PDFs is for the application I am developing essential. As hundreds of historical documents are catalogued and can be opened in the 'window viewer'. The user will than search through documents in the PDF (which has been passed through an OCR program). Now by copy & paste parts of the PDF document can be selected. It is essential that these selected parts are marked for later use, or use by others, who thus can know these parts have been processed already.

I have tried several ways to get this working (also making Adobe professional 9 the Adobe reader preference of the Safari browser on my system (I think FMP uses that info to determine what PDF reader to use. 

I can not get it to work. I think that having this functionality would be a great enhancement for work with non-standr older historical documents ... So I would pleased with some insight/suggestions.

Now I have to do the marking by having Adobe open external... (I can trigger - of course - Adobe Pro to open a specific file on a specific page (using Applescript) and when I later (re)load that file in the web viewer.. it shows up nicely... Thats is not really an integrated solution.