@teamfraught: I recommend GoodReader for PDFs. It supports annotations, and Marvin can load PDFs from your Dropbox folder to GoodReader as you request.
You can use the
Annotations plugin to archive annotations from both Marvin and GoodReader in calibre.
Converting PDFs to epub format is an exercise in frustration which rarely yields good results. It's less frustrating to simply read the PDF content in a reader optimized for PDF.
G