FM3 and ENGL multiple fx loops

Hey, good people. I got my new FM3 yesterday, and I am putting together a crazy pedalboard. I control everything with a BOSS ES8, and my amp is an ENGL Special Edition with 3 FX loops (2 parallel, and 1 series). Anyway my plan was to have one of the FX loops utilizing the ENGL's tone, and then connect the FM3 to another FX loop (return), so as to bypass the ENGL's pre-amp and use the FM3's amp models.
Now, the FM3 works, and the amp as a power amp works as well. The problem arises when I add in the rest of my gear. The loop that has the FM3 in works as it should but when I switch to the other loop, the FM3 is still coming through. I may very well be missing the totally obvious, it's been known to happen, but for the life of me I cannot see what I've put in wrong. Is my theory right in the first place, or am I imagining something that cannot happen?
Oh, and please, I'm a visual learner, I find explanations so much easier if I can see what's going on or hear the explanation, so make your explanations REALLY simple.
Many thanks.
 
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