The National Institutes of Health (NIH) have four methods of submitting articles for compliance with the policy.
If using the NIHMS system (ie, you are depositing your article instead of the publisher), the NIH has provided helpful tutorials to help guide you through the publication submission process. See their tutorial page here: http://nihms.nih.gov/db/sub.cgi?page=stepbystep and an NIHMS online guide here: http://www.ncbi.nlm.nih.gov/books/NBK3845/
To check the compliance status of your publications, first you need to make sure you have a My NCBI account. There is a comprehensive guide to My NCBI on the NIH site here: http://www.ncbi.nlm.nih.gov/books/NBK3843/
This account can be linked to an eRA Commons account.
Use the My NCBI "My Bibliography" feature to manage compliance. There is a helpful tutorial on the NIH website here: http://www.ncbi.nlm.nih.gov/books/NBK53595/#mybibliography.Checking_your_Publication
The PMCID or the NIHMS ID can be used to show compliance. The PMCID can be found by checking your publication in the My Bibliography section of My NCBI, or by searching for the publication in PubMed. The NIHMS number can be found in the My Bibliography section of My NCBI if the publication has been submitted, but has not yet finished going through the Pub Med process.