I just noticed this thread and thought i'd share my experience....
I've always used lots of pedals and distortion. I always thought what I needed was one amp for clean, and one for my pedals. One day I actually got to try it, and it was awful. So, I tried running the full range of my pedalboard, blended with a small amount of clean, all into a large full range bi-amp rig. That sounded amazing.
So, perhaps a bi-amp rig will get you the sound you want, but I would do your crossover after your pedals.
From the above I assume you've just got the full range of your board into the full range of 2 amps, which will no doubt sound massive. Nice!