We use Zotero to organize manuscript references and add these references to our manuscripts, grants, and other lab documents. Zotero has a stand-alone app, a web browser extension, and a plug-in for Microsoft Word and Google Docs.
You should keep a personal library using Zotero, which you can do by creating an account. The benefit to this is that you can sync this library across multiple computers which means you'll always have your references at your fingertips!
When it comes time to write a manuscript, we have a Sammons Lab shared Zotero group that will allow us to keep our references straight.
Zotero makes it pretty easy to import manuscript references into your library.
You can add a reference right from PubMed.
You can add a reference from the journal webpage. This has the advantage that Zotero tries to download the actual PDF (if it is available to you) and then stores the PDF in your Zotero desktop app. Very very handy for keeping track of your PDF files.