Hi Brian,
Yes you can mark up PDFs, a couple of way. The built in PDF Reader has rudimentary mark up support, Black Ink and Highlighting. You can use PDF Touch which has more options. What I typically do depending on use case, if it is for me only, I send the PDF to OneNote and mark it up there. If I need to share the PDF with others, I use Word 2013 and then save it back as a PDF.