You can open a PDF on the LCD screen with DoctoGo or a PDF reader like Repligo, BeamReader etc, provided it is not a PDF with DRM. You can open a journal on the reader side at the same time and make your notes, however, there is no way to annotate, or mark a page in the PDF on the LCD side.
You can reverse the process and open the PDF on the reader, now use a note taking app on the LCD to make your notes. You can attach pictures (which have been added to library) to your PDF file at the point where you wanted that note to be, so if you use an app that saves in a picture format, you can attach your note to your marked PDF file. You can also attach word documents created in DocstoGo after adding the .doc file to the library.