I personally do not like pdf's indexed since when found in search engines the pdfs do not usually contain links to the regular site (say the home page) I usually like to put the pdf out there for an option but still have at least include an html version of the pdf on my site.
With that in mind, you could look at you stemap XML file and just add the pdf's youself using a regualr text editor, or even an html editor. You will easily see the make-up of the xml file
I do industrial search engine optimization and always advise my clients to have both an html version and the corresponding pdf