If you are looking to add a custom master page to all new My Sites, there is no way to do this by default. The following article describes how to do this using a “Feature” in MOSS 2007:
This article is very helpful, but you should know you can skip to the end of the “Installing” section to find that all of the work has been completed for you and put into a solution file on CodePlex.com:
This solution is useful, but there are a few issues with it and improvements that can be made which I will soon discuss in other posts.
One key thing to take away from this is the existence of Features, and the Stapler/Staplee method of applying features to MOSS 2007.