I've started to look at patching the General controllers but I have one question:

What would be the preferable way of setting up the General controllers so they don't conflict?

For example, GC1 users two channels - 1 & 2. GC2 users 2 & 3. So if they are patched through the same universe the second channel on GC1 conflicts with the first channel on GC2.
Is it a case of patching the controllers on alternating universes to stop this conflict or is there another way around this?