Keep in mind that it's the publisher's policy that determines the Journal Method. You don't get to choose the method.
Author publishes in a journal that submits all NIH-funded final published articles to PMC; no fee for submitting to PMC, but these journals often have required Author Publishing Fees. List of Method A journals.
Author requests the publisher submit an individual NIH-funded final published article to PMC; often fee-based service.
Author self-submits the final peer-reviewed manuscript to the NIH manuscript submission system (NIHMS); no fee.
Publisher submits the final peer-reviewed manuscript on behalf on NIH-funded authors; no fee.
Not sure what method your journal is using? Feel free to ask Kate Anderson.