Potentially, but only in the effected signal. The dry signal would not be mixed together. A lot of the effects are true stereo, too, so it would depend on what effects you're using and how you've got them setup. I think the best thing to do is to try it both ways and see which you like best.
As examples, in my practice rig, I've got a MB Mark IV combo feeding my pedalboard, which then goes back into the return on the main amp and the return on another MB combo. In this case, I'm driving both amps with the primary Mark IV.
In another rig, I've got a Marshall DSL and a VHT CL50 running in parallel. I feed my pedalboard from the sends of both amps, which goes back into the returns of both amps. In this case, each amp is contributing to the sound. Channel switching is done via MIDI with a custom cable for the VHT (the DSL uses 1/4" jacks).
