sup guys, ive been having this same issue with my mesa rectifier. i tinkered with it a bit and this may help you guys out.
you have to go into controls and assign a foot switch to ext amp. then set it to 1 (tip) or 1and2. 2(ring) i couldnt get to do anything.
but when you do this it only works on the stomp presets. for example, when you pick weather or not you want snap/preset or snap stomp be sure to have stomp on there somewhere. then like i said assign it to a switch. now this next part is important, when you assign it to a switch hit the save button. at the bottom of the screen you will be givin an option on where to save it. for example 1a,1b,1c ect. be sure to save it to a switch that is in stomp mode. these usually have no label on the little tab screens. once done the tab should say ext amp. now press it and bingo. your channels switch.however i still have not figured out how to set it up to where you can have one switch to dirty and one switch to clean. the problem im having is once you switch on channel 1 and then click the other assigned switch to channel 2 it leaves on both channels instead of switching the other one off. so atleast the channels are switching atleast lol.