So playing with this a bit -- First -- I LOVE IT! Great work :). One bug found so far:
Buildcraft pipes don't work with items going INTO the machine. Regardless of the pipe going into the Top, Bottom, or Side, it always tries to put items in the output slot.
Wooden pipes on the side DO pull from the output slot, so thats good :).
Note that if the Output slot is occupied, items filter into the battery slot next.
Typically buildcraft has items work like so :
Pipe into the top - Top input slot (Where you'd put items here)
Pipe into the bottom - Bottom input slot (Battery)
Pipe on the side - Output slot.