Not a stupid question at all. When they install the aftermarket muffler they can either cut off the valve and hand it to you so it can be reinstalled later if need be, or they can leave it. They are located behind and in front of the OE muffler (if you have a 6.2). I doubt there would be much of a performance difference if you leave them, however it will be quieter due to the restriction. I say cut them off, weld on the new muffler, give it a chance to break in and see if you like it. If it's too much, they can weld one back in. If it's still too much, weld in the other one. I would leave the resonators, they are straight through and don't offer any performance advantage if you cut them off.