Management of pdfs and how mendeley finds new annotations

Hi! I have Mendeley installed on my desktop, and have NOT clicked in the Option - File Organizer - Organize my files. This seems to mean that all pdfs, that I typically store in a folder called Research/Articles, are copied by Mendeley into another folder, managed by Mendeley. So.. what happens when I make a new annotation to an aldready existing PDF? It seems that it is not found by Mendeley, which makes sense, since I have annotated it in my folder Research/Articles, and a copy of it already exists in Mendeley's own folder. So how do I manage this? What I am after is not to add new pdfs, but to make Mendeley identify new annotations, made with other programs, in the PDF-files (I annotate using an Android tablet). Magnus