The NIH has a number of resources further explaining their policy and processes:
PMID = permanent PubMed abstract identifier
PMCID = permanent PubMed Central full-text article identifier
NIHMSID = temporary manuscript submission identifier given to an author who self-submits a manuscript to the NIHMS system
PMCIDs must be included when citing papers in NIH applications, proposals, and reports.
Either the NIHMSID or the PMCID are acceptable for proof of policy compliance within the first 3 months after publication. After that, the PMCID must be used. The PMCID always supersedes the NIHMSID.
Compliance status will be displayed in the "Manage Bibliography" view of "MyBibliography" within MyNCBI. You can add or revise compliance status there. Additionally, grant awards can be linked to citations there as well and lists of citation by grant award can be generated.