Hey Bec,
Each program with a published MSI email is a folder. So in my instance, we only have one because we are tracking MSI emails on a high level - one program. But if you had multiple programs, as long as the MSI email was a local asset, they would show in the main dropdown as folders.
Then under each program you can make folders to organize. I'd recommend creating a test program or two and emails to figure out the configuration you want before actually building it out.
Kim
NOTE - this doesn't work the same in the Outlook Plugin though.