I have a Peavey special transtube 212, the pedals I have a a boss super chorus, metal muff and cry baby. Now when I turn on the metal muff I get a little feedback that seems pretty standard when there is distortion or OD present. My question is this, I have just been running my setup like this since I bought the amp:

guitar>crybaby>metal muff> chorus>amp

however by running it this way I have just been switching to the clean channel when I have the metal muff on which causes some tone issues, because I not only have the eqs on the metal muff to set but also the amp channels eqs. So I played around with the fx loop tonight and had it set up like this:

FX send>crybaby>metal muff>chorus>FX return:

and then my guitar runs to the high gain jack on the front of my amp. When I have the metal muff running through the fx loop in the order stated above and its turned on there is quite a bit of noise coming through the speakers but its different than that distortion feedback sound, its just loud, if that makes sense. So basically im wondering should i be running the metal muff through the FX loop?
No you don't run Distortion through the FX loop. You only run effects that need to happen after the distortion like wah (if you want it that way) delay, chorus. It's better to delay a distorted sound then distorting a delayed sound.