Qubes has its OS specific package manager to deal with the admin Qube for specific packages, but that generally isn't your priority and shouldn't be touching that part of your system.

Everything else runs in VM's. Yep VM's with their own filesystems (there are ways to pass files through each though). By default, Qubes has Debian, Fedora and Whonix installed, but the community has Qubes templates for other software. You could also use a VM for other OS's youre comfortable with.

The fact that everything is VM's is you can experiment with different systems, versioning them. If you mess one up, you can delete and clone the Qube from the previous version.