Banks puts a lot of stress on the head gaskets and doesn't actually tune the transmission. After I blew my head gaskets, I got head studs and switched to a custom tuned SCT.
Banks runs ok at the lower settings but the SCT is safer for your truck.
To answer your original question, put the Six Gun setting to "1", disable Speed Loader and you will be fine to take it to the dealer like that. They will unplug the OBDII, which is fine. Usually they plug the Banks back in, but if not, just plug it in when you get it back.