In the sanctuary there are some locked doors, in one of them, (after lockpicking) there is a church key. I've tried to find out what it does, but I still don't know. Does anyone know what its used for?

Thanks in advance, Portent

Some of the doors in the church are locked, and un-pickable. You need the church key to open those ones It gives you access to every door except the confession box one.

is there anything in the church once you can get in those rooms?

Not really, but it makes moving through the church alot easier