Authors, PIs, or someone they delegate can submit the final peer-reviewed manuscript (not the final published version) to the NIH Manuscript Submission System (NIHMS). Basically a six-step process, the NIHMS process can take approximately 2 to 3 weeks following initial approval of a completed submission.
The NIHMS Step-by-Step Tutorials illustrate how to perform various actions in the NIHMS system:
The Deposit and Initial Approval video provides a detailed demonstration of the manuscript submission process, including how to associate funding, upload required files, and approve the submission for NIHMS conversion to PMC-ready documents.