I want to play some media files with certain subsessions in our show. Is there anyway to link the loading, or muting/unmuting, of certain media file with the loading of certain subsessions?

Absolutely!
Just tick a media file and it will be available to play. There are ways to autostart a file when a subsession loads too.
Is that what you want to do?

I want to make certain audio files load and be ready to go when I load certain subsessions. But, I don't want them to auto-start, I want to be able to start and stop it during the song via the master transport controls assigned to switches on my keyboard.

How do I set that up? I didn't see anyway to set the subsession behavior for media files.

Thanks

Follow-up:

I ended up setting up Midi Assignments to start and stop each track from two switches on my controller, and set all of the assignments to be enabled/disabled via subsessions. Now I just have to make sure that only the one I want is enabled in each subsession. Works well, but is kinda tedious to set up.