What tool can I use to manage notes and/or bookmarks for a collection of PDF files? I am doing some research and I do put lots of notes and bookmarks in the books (PDF files).

I am looking for a tools that will allow me to see and search inside all these notes.

I supposed that this tools should be able to scan a directory with PDF files, for notes and keep them in sync.
You should try Mendelely, a Reference Manager with Dropbox-like sharing/syncing. It reads Comments from PDFs, but sometimes mixes them up. In my example i had saved an Article as a PDF with the Headline as the Filename, but Mendeley indexed my Comment as the Filename. 

You should also take a look at Eaglefiler, as the name says more Archiv-oriented.