I sent this earlier this week via email, but upon checking my Junk Mail box I found a message that it failed delivery. Here is my reply:
Here is my signal flow/setup for the M13 regardless of the amp I use it with (which is several):
Guitar > M13 Input > FX Send > Amp Input > Amp FX Send > M13 FX Return > M13 Output > Amp FX Return
This setup allows me to use FX row 1 in front of the amp and the other 3 in the loop.
I don't use any of the MIDI functionality, I literally treat it as a stomp box pedal board and step on what I need like a bunch of pedals. Any switching for the amp is done via the amps dedicated switch. I really don't use any MIDI these days unless the amp pedal uses it (like the RM100). I am not even aware of what MIDI capability the M13 has honestly, as I never use it. I'd probably look to the Line 6 support forums for help on that.
Hope that helps,
Rob