Most things should be behind Authelia. It’s hard to know how to help without knowing what exactly you’re doing with it but generally speaking Authelia means you can have SSO+2FA for every app, even apps that don’t provide it by default.
It also means that if you have users, you don’t need them to store a bunch of passwords.
One big thing to keep in mind is that anything with its own login system may be more involved to get working behind Authelia, like Nextcloud.