Are they all really hooked via MIDI? I mean, they're just some older 'dumb' midi devices not USB-equipped gear? What virtual amps do you mean???
I've never used that much MIDI, only some controllers etc. but they've been very simple to set up. Just plugin from outs to ins of the next device in most cases. There's no use using the midi thru I understand if the end device only has one port anyway. You would use the thrus when for instance when you have two rack effects controlled via MIDI; you don't want the first device's output to go to the next device in addition to what the controller sends.
BUT if they're all going to the same end device, you need to send all the device's commands there.
Further, I understand no matter how it's set up in the end, it's a case of finding out what signals will be going to the computer and then map each MIDI signal to the desired command in the software. For instance I map one device so that one generic button changes track, another does undo, third play etc. etc. and on another device I have sliders mapped to DAW channel faders and such, and for that I got some ready-made presets for Cubase off the net.
I might be wrong, but I believe in case of the computer, it doesn't really matter what midi channels the devices use, you just need to map the signals on the computer to their correct functions. BUT you must set each device to use a different channel so they don't overlap. In case of actual devices the send device and the receiving device must use the same channel, though, but also there you'd program the end device to respond as you like when it gets a certain MIDI command over the link. This is just guesswork - I do not know if the MIDI interface you have will only accept signals from one channel at a time or all.
I haven't really used anything true MIDI with any of my gear in ages except to do a MIDI dump from device to device to save settings or remote-control or sync two FX boxes, it's basically all hooked up via USB...I did have a MIDI keyboard/PC card system back in 1998 but I thought it had pretty much died since that in PC world and everything just uses MIDI over USB.
Currently I use a mixer device, a remote controller and a keyboard in my DAW, all sending MIDI over USB.
Well I guess this wasn't very helpful, sorry...:-)
Dee
"When life's a biatch, be a horny dog"
Amps: Marshall JVM 410H w/ Plexi Cap mod, Choke Mod & Negative Feedback Removal mod, 4x12", Behringer GMX110, Amplitube 3/StealthPedal
Half a dozen custom built/bastardized guitars all with EMG's, mostly 85's, Ibanez Artwood acoustic & Yamaha SGR bass, Epiphone Prophecy SG, Vox Wah, Pitchblack tuner plus assorted pedals, rack gear etc. for home studio use.