Some publishers will deposit an author's final published article in PMC upon their request. These journals do not automatically deposit every NIH-funded paper. Rather, the author can arrange with the journal for the deposit of a specific article; this usually involves choosing the journal's fee-based open access option for publishing the article.
It is the author's responsibility to make arrangements with the publisher for this service via that publisher's copyright agreement form. If the author exercises this option than no further action is required except to cite the PMCID number in future NIH applications, proposals and progress reports.