Ugly Bunny
Power User
This is what I do with my King of Tone; Out/In 3 Right goes to KoT's Red side, and Out/In 3 Left goes to the Yellow side. Then I can use the same I/O block(s) and just set up channel A to pan left (Yellow side) or channel B to pan right (red side). I don't stack the pedal's sides so that's not really a concern, though I wonder if it's possible...You could also put a couple of pedals in loops 3 and 4 prior to the amp block and switch them in and out using scenes/presets.
In any case, I've found pedals to work best in the loops, NOT going into Input 1.