I used to have the version one. It was super simple to program. You just go to a preset on your midi controller, switch through the channels on the M4 using the channel button. When you have the channel you want for that preset you would then hold down the channel button for a couple of seconds. It should be stored after that. Hope that helps.
I'd speak directly to Bruce on this if I was you - his emails on this forum and in the MTS one too. What are you trying to achieve via midi, channel selection is pretty straight forward (as detailed in the post above) but something like setting the midi channel for the preamp is a bit more involved - from memory you need to take the top off and set internal dip switches to do that.
Give us some feedback on what your up to and we can hopefully point you in the right direction