The NIH has a number of resources further explaining their policy and processes:
Manuscripts that fulfill all of the following criteria must be submitted:
Manuscripts accepted for publication before April 7, 2008 may be submitted if authors have the appropriate copyright permissions and all other criteria are fulfilled.
Authors are responsible for compliance with the policy. You must make sure that all publication or copyright transfer agreements that you sign will allow you to submit your manuscript to PubMed Central. If possible, work with publishers before rights are transferred to prevent later problems.
See the Journal Policies section of this guide for more information on how different journals handle submission to PubMed Central.
At present, UF doesn't have any standard forms to add to publisher copyright agreements.
The NIH provides an example of the kind of language that can be added to a copyright agreement at http://publicaccess.nih.gov/FAQ.htm#778:
Additionally, the SPARC Addendum is commonly used by authors. Information on the addendum and the addendum form itself can be found here: http://www.arl.org/sparc/author/addendum.shtml.
Similarly, ScienceCommons provides information on publisher agreement addendum: http://www.sciencecommons.org/resources/faq/authorsaddendum. ScienceCommons also provides an "Addendum Generator" where you can put in the information and it will generate a addendum form.
More information on author's rights in journal submission can be found in the Author's Rights section of the Open Access and Open Access Publishing Fund LibGuide at http://guides.uflib.ufl.edu/content.php?pid=109174&sid=833882&search_terms=author%27s+rights.
The NIH states that it has not yet encountered a publisher that refuses to comply with NIH policy. However, this does not mean that you won't encounter one. Contact the NIH at PublicAccess@nih.gov for more information and assistance.
Also see the UF Libraries guide to author's rights and copyright.