Can the Transit be used as a channel selector for an amp head? Also where would a tuner pedal go? Thanks
No, and wherever you like. That's the point of a pedal looper, you can put pedals wherever you need them to be.
I'd suggest trying it in front of the looper, i.e. not in any of the loops. That way you can mute everything with the tuner, no matter what else you have going on.