When I had this running, I skipped out on the extra boiler, and set up a still next to the fermenter. Produced about 1k of biofuel, which gave me enough to start playing around with the IC2 armour (the gravi-suit and similar, I know it's not strictly IC2, but it's close enough).
I find that, when you have a glut of BC energy, you're better off making something storable and interchangable (I can use the biofuel in bio-generators or combustion engines, as I see fit).