MIDI to sync Preset and Scene between the two units is not hard at all to set up.
Control Switches can send MIDI CC values 0/127 to indicate on/off, so if you assign the CC numbers carefully, you can end up with 12 CS available in both units.
Continuous controllers are not shareable between units unless you use a unit like the ExpressionIO and move them out to MIDI. Upside, your DAW can record your controller moves so they can be used when re-amping.
Have not yet found an easily configurable way to trigger channel switching in the FX3 yet. Might need to look at a more configurable MIDI unit to do the same things that a Fractal channel switch can do. There is a way to do it, but it is a direct channel selection for a particular instance of a particular block globally, so the best that can be achieved with the ExpressionIO is alternating between two channels on the same instance of the same block in every preset, i.e., Delay 2 or PEQ 1. Maybe one of the Arduino projects can be leveraged to get some flexibility of capability to mimic the Channel Switch capabilities from MIDI switches.
I wish MIDI switches could be stand-in switches.
For now, I have an FC6 hooked via FASLINK2 to the FX3 which can do Channel Switch stuff for the FX3.