Voodoo Lab

Ok...so after about 9 years of dreaming and, little by little, building this rig I finally feel like I got in over my head with my ambition for this rig to do everything I need it to do. This is my first time getting into the GCX and Ground Control world (I was previously using an old school Mesa Abacus until that finally stopped working) and what I would like to do is use both my rack mounted effects processor along with some analog effects and have the Ground Control Pro command it all. Here's what I'm thinking the flow chart would look like

Guitar > GCX> Boss NS-2> TS808> Boss CE-20> Flanger> Preamp

Preamp> FX LOOP> Boss GE-7> Boss GX-700> Mesa 2:Ninety

My questions are:

How would I wire something like this up?
Would it make this whole thing easier if I dedicated one preamp to cleans and one preamp to distortion and if so, do I need a second GCX processor?
How do I make the Ground Control Pro control both preamps and GCX effects?

Below are some pictures of the rig in question:

You have a lot of cool stuff there. I'll try to help where I can, but it's not totally clear what you want to do with all of this.
The Tri-Axis is MIDI controlled so I don't think there would be much benefit to dedicating one to clean and the other to dirty... perhaps another boardie here has an opinion on this (some of you have to!)? I guess that would all depend on how the Tri-Axis handles switching between clean and dirty patches. (anyone else do it this way?)
I see only 7 things to be switched so I don't think a second GCX would be needed... 4 front end Pedals, Preamp A/B, 1 pedal and the processor in the FX Loop... 7 GCX loops total.
Programming this would require that each MIDI device is assigned to its own MIDI channel. This is covered in the Device Name/Channel section of the Ground Control Pro manual under Setup Mode.
For wiring check out some of the rig diagrams here http://voodoolab.com/gcx.htm for the different concepts or ways the GCX can be used. Also, be sure to check out the rig pics on this forum for some fine examples of how a finished rack looks from the back once Mibu or Trueman have gone to town.
Keep us posted on your progress!

Thanks for the reply John. I will take a look at some of the finished products and I will get back with you. I'm working on this rig on and off during the week so I'll keep you all posted. Thanks!