I saw that you can use a mailpress-config file to move the location of
Mailpress theme files. But it wasn't super clear on how to do it and
didn't seem to answer exactly what I wanted to do, which was move all
of the Mailpress themes into the theme directory of the site they
belong to. Worked up a solution to it I thought I'd share in case it
helps anyone else out.
http://newportcreativegroup.com/blog/2010/12/02/let-mailpress-themes-live-in-your-blogs-theme-directory/
Now all of my email templates are right alongside the rest of my
themes, safe and sound from future upgrades and my various site users
only see files that are applicable to them, not every Mailpress theme
in the multisite install.