The setup I use is:
Output of a SC2 farm on the border of a chunk is pumped out.
First destination is a squeezer for apples. The juice and mulch is pumped to a fermenter (when full, the mulch carries on to a second filled with water). These are where the saplings are put. The tree farm output then goes to barrel/void.
The biomass is pumped from fermenters to 3 stills (usually the limiting factor for the system), then into a xycraft tank underground.
To begin with, this is powered by a biogas engine attached to the line, but now I've got the wood excess cooked by a powered furnace, feeding a 2x2x3 LP boiler, giving more than enough power for operation, and to develop my systems further.