The NIH has a number of resources further explaining their policy and processes:
To comply with the Public Access Policy:
There are multiple methods of submission to PubMed Central, depending primarily on your choice of journal. Find out how the journal handles compliance with the NIH Public Access Policy in advance: make certain that your copyright agreement with the journal allows for compliance.
The NIH strongly recommends that investigators utilize the MyBibliography tool within MyNCBI to list all citations that will be used in NIH grant applications, progress reports, or proposals, or are generated from those grant awards. At present, it is not required, however at some point in the future, the NIH plans to have My Bibliography replace any other method of entering publications into eRA Commons.
The use of MyBibliography allows the user to link articles both in and outside of PubMed to grants, to easily view compliance status on all articles, and to rapidly generate lists of articles by grant award in pdf format. All grant-linked articles in My Bibliography are automatically imported into eRA Commons. Also, once a grant has been linked to a citation in MyBibliography for one author, the grant association to the citation will automatically appear linked in the MyBibliography of all authors. This is extremely helpful for articles which did not originally cite the grant award.
Note that it NOT necessary for an article to be in PubMed and have a PMID for compliance. An article that is not in PubMed can be added to MyBibliography and linked to a grant award. The requirement for compliance is that the article is in PubMedCentral and has a PMCID. See the "PMCIDs" section of this LibGuide for more information on the difference between a PMID and a PMCID.