Think this is about as nice as I will get the tree farm piece:
Same basic pieces, but moved the pulverizer over a relay. It outputs the red output (sand and saltpeter) into the relay -- which gets it into the pipe system. Saltpeter and sand goes to the wooden double chest used by the the sandstone and fertilizer autocrafting tables. I had to use some covers to keep things separate, but it all fits well and all the chests/inputs can be access to load extra sand into the system. If you want extra humus.
The pulverizer yellow output (niter) just loops out the side and into the hopper.
Autarchic gates for the screenshots. Redstone engines will work just fine in thier place. Dirt in the barrel, but could be any container. If you use a different container you might have to move it to another side of the humus auto crafting table to avoid the pipe return to the relay.
Fairly simple and very effective.