It's probably dependent on the pedal, though I would think most would have the adjustable tone section after the distortion circuit. After all, doing it before wouldn't prove much advantage over using your guitar's tone knobs, and the clipping will generally create harmonics that may or may not be useful, so a filter is usually put in afterward to help smooth out some of the harshness.
Some will have a hard wired EQ section. Something like a bass or treble cut before the clipping starts. I think the Tube Screamer has a HPF to cut the bass before it hits the first gain stage and then the normal tone stack after it. I'm not sure though. It's been a while since I've seen that schematic. Some pedals have more than one clipping section, so that would give you the opportunity to place an EQ in the middle. I think the Big Muff has multiple clipping stages, IIRC, but I think the tone section lies after both stages.