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/