No matter what I or anybody else says about how things are "meant to be", it's always worth experimenting to see which way works best with the specific gear at hand. Neither the amp nor the fx will be damaged by that experiment!
+1 - If I lower the input level of my preamp, I can actually use my Clone Theory in the loop without issues. That's also where it happens to be its quietest, and it sounds quite good there. However, my tone is dependent on a higher preamp gain level, so it doesn't work for my situation.
Hmm.. all good thoughts.. I guess I should try putting the Big Muff first in the chain before the Zoom - I always figured it was better to use distorting after the other effects, but perhaps my thinking is wrong in this?
Most guitarists and bassists actually place other effects (like delay, chorus, etc.) after distortion, from what I've seen. However, it never hurts to try it the other way. Take the band Death From Above 1979 for example. The bassist used a chorus pedal in front of two solid-state amps pushed to the distortion point, and it sounds awesome.
There's no hard and fast rules for this kind of stuff. You'll see it gets especially complicated with people who use both overdrive and distortion pedals and combine them. Some people like it in one order, some people like it in another.
Also - given the issue I am encountering, would it be advisable to use the Big Muff direct from my bass and then into the amp, and stick the Zoom through the loop, or vice-versa?
Yeah, I'd put the Muff out front, as it's particularly sensitive to the input level. Many fuzz pedals don't like the high output of active basses... so you could imagine how much a preamp's output could adversely affect the Muff. My Little Big Muff works fine with active basses, but others have had issues with it and other fuzz pedals with active basses.
As for the Zoom... if it can handle the output of a preamp while still pumping out a sufficient output for the poweramp, it could easily stay in the effect loop. I'd highly recommend trying it out front first, both before and after the Muff; after all, it's a multi-effects unit, so you're dealing with a lot of possibilities. See where you like it better, and remember you'll have to adjust its output level accordingly!
Personally, I'd do Bass => Big Muff => Zoom B2.1u => Amp Input.