I'd say use the pedals you normally use, I kinda prefer clipless but have used both. The potential downside of flats is you can sort of leave the pedal behind on the upstroke in those udgy moments when you're grinding away at 1/2 an RPM.

Also, get your chain as short as possible (esp with a ramped chainring) and try and get a good chainline. You might even think about a half-link in the chain if you don't fall lucky with the chain length. Charlie bike monger has them.