I don't have an MT15, but I have an Archon and they're very similar. The amp has a ton of headroom no matter how it's set. I prefer my Archon clean channel with the gain on max. Even with the gain on full, I can take a klon-style overdrive (which have enormous output level), maximize the boost, and it still won't be enough to get the preamp to distort.
If I'm using pedals for distortion, then I like the bright switch on the Archon off. The MT15 doesn't have a bright switch, but I'd start by keeping the treble boost off when using dirt pedals. I'd imagine that distortion pedals will sound really harsh with the treble boost on, but experiment yourself and trust your ears.
As for bass/middle/treble, I would just set it so that it sounds great dry and adjust the pedals to work with it.