You do not need to submit your manuscript if you publish in one of the journals listed here.
Otherwise, submit your paper at NIHMS, the NIH Manuscript Submission system. (Log in with your eRA Commons account.)
Instructions for submission, including screen captures, can be found in The NIHMS System User's Guide to Submitting a Manuscript on the NCBI BookShelf. Videos are provided to demonstrate the submission process and manuscript approval. NIH also provides some very good tutorials to guide you through the process.
Final Peer-Reviewed Manuscript: The investigator's final manuscript of a peer-reviewed article accepted for journal publication, including all modifications made by the author from the peer review process.
Final Published Article: The journal's authoritative copy of the article, including all modifications from the publishing peer review process, copyediting and stylistic edits, and formatting charges.