So you want to be able to switch between (for example) channel A with stomp boxes and channel B with no stomp boxes?
What kind of effects would you be using? If they are modulation effects, delays, etc then something with an assignable effects loop or a separate loop for each channel would work.
Perhaps an amp with MIDI control such as the Hughes & Kettner Switchblade might be able to do this?
If you're planning to use overdrive/distortion/wah or any other pedals in front of the amp you might be looking at a 2 amp setup and an A/B switch, unless you can find a loop pedal that also allows amp channel switching.