Regarding using a clean sound with pedals - this is what I would do. I usually will run my signal via my pedals, and into a completely flat-EQ clean sound. Then, if I want filth, turn the gain up on the clean channel, until I get the bite that I want, and roll the master volume down to a suitable level, and EQ/Touch up as necessary.
My amp has 2 channels, but I run my pedals into the clean channel, then just add gain to that clean sound, if I want more bite. A clean sound really does receive pedals best, in my opinion, much better than messing around with doing anything fancy and intricate with your amp.
Regarding using a clean sound with pedals - this is what I would do. I usually will run my signal via my pedals, and into a completely flat-EQ clean sound. Then, if I want filth, turn the gain up on the clean channel, until I get the bite that I want, and roll the master volume down to a suitable level, and EQ/Touch up as necessary.