I use zotero and store the pdf files (renamed and organized with ZotFile) on OneDrive. I can read papers and make highlights/notes to pdfs and they will sync to all of my devices. These notes can be extracted and made searchable within Zotero by Zotfile.

At first I preferred the way that Mendeley did this with its built in pdf reader, but now I'm happy Zotero delegates to the pdf software of your choice.