Copyright Basics
When submitting a manuscript to be published in a journal, the author(s) will be required to sign an agreement to either grant the publisher the right to publish, or relinquish the copyright altogether (many cases). Before signing any copyright agreement, MAKE SURE that it provides permission to comply with the the Public Access Mandate. Keep a copy of the agreement on file!!
Publisher Requirements
Some publishers will submit the manuscript to the designated repository (e.g. Pubmed Central) on behalf of the author(s). Look for a place in the copyright agreement, or an accompanying document, to indicate that you are in need of that service, and any additional information required to complete the deposit accurately.
Other publishers will have very specific instructions and stipulations for author(s) who need to deposit the manuscript on their own. Follow those instructions as they are the terms of your copyright agreement.