Parallel Setup Switching

[Swimming Bird]

People who use multiple boards in parallel: how do you switch between your boards?

I'm running two big pedal chains out of two different outputs on my main instrument (a double neck steinberger rip-off) and end with a home made double kill, double switch box. It works fine with a mixer, but when I try to not drag that around I get ridiculous amounts of noise (each channel of the homemade box then just acts as a kill going into the stereo input of an RC-50). Am I missing something obvious or does everybody have a more or less unique problem?

Thanks.