Ah, I misunderstood you then. You're talking about bypassing the amp's preamp section completely and going guitar --> clean boost pedal --> amp power stage. I thought you were talking about running the preamp output into the pedal and then back into the power stage, thinking that the pedal could "clean up" the signal. As long as the pedal has whatever tone-shaping controls that you need and enough output to drive the power stage, that should work. I still think that a different amp would offer you greater flexibility and control, but that's your call.