I'm running mine in the effects loop after the pre-amp (I'm not using any Dist/OD pedals, so it's all coming from the pre-amp). I have run it in front of the amp, too, though. Both sound great, but do sound different. The effects loop works better for me in my current rig. That's subject to change, though…
I don't think either in front or in the effects loop is any more or less valid than the other, but rather, what sounds best to your ears and works best for you in your rig.
