Muppeman, I know this is an old thread but I have your exact setup with a Musicom Lab EFX LE and an HX Stomp. Trying to figure out how to run these using 4CM but not having any luck, so far. Right now I am trying to run the first few loops from the EFX into the Stomp and then run the modulated loops from the ISO OUT into the Stomp's FX send/return. I haven't been able to figure out how to get a loop or loops to only play through the ISO OUT. If you were able to figure this setup out and remember, please share how you did this. In the meantime, I will try what Kilrahi shared.
Thanks!