A fermenter will turn saplings, water or apple juice, fertilizer (or compost or mulch, if I remember correctly- although I think the nonrenewable stuff gets you the most biomass- though I'm not sure as to whether that's per sapling or per fertilizer), and up to 16 or 17 MJ/t into biomass. Biomass can be burned in Biogas Engines for 5 MJ/t or the Bio-Generator for some EU.
A still will turn 10 buckets of biomass and up to 5 or so MJ/t into 3 buckets of biofuel, which can be burned in the Bio-Generator (not sure if it's more efficient to burn biomass or biofuel in this machine though, considering distillation costs) or a Liquid-Fueled Steam Boiler from Railcraft.
As to wooden pipes, charcoal, and furnaces, BC pipes are rather stupid. I would recommend placing an Iron And or Or Gate (made in the Assembly Table) on the pipe beneath the furnaces. Run some Red Pipe Wire (also made in the assembly table and a component of the iron gates, one craft of them will probably be enough for your purposes) along the pipe from both furnaces to the charcoal chest. On the wooden pipe, you'll need another iron gate- I'd recommend upgrading this one to autarchic, although you could use a normal iron gate and a redstone engine. The pipe under the furnace nearer to the chest should be diamond, so you won't lose items.
Configure both gates on the furnaces to "Inventory Empty" -- "Red Pipe Signal", and the one on the wooden pipe to "Red Pipe Signal" -- "Energy Pulser" or "Redstone Signal" if it's not autarchic, to power the redstone engine.
Thus, when either furnace runs out of fuel, it will tell the wooden pipe to send more. BC gates will only detect items in slots accessible from the side the gate is on- in this case, the fuel slot.
Or, you could just replace the iron furnaces with electric or powered furnaces, depending on whether you're powering your farms with EU or MJ, or throw in another power system and use free energy for Bluelectric furnaces or Factorization-heated stone furnaces.
EDIT: As I said earlier relating to overflow and BC pipes, use diamond pipes. Unless you mean producing more charcoal than the furnaces use- you could use MOAR gates and an iron pipe to send excess wood somewhere else, when hoppers on top of the furnaces fill up.
I've heard that in order to get a gate-controlled iron pipe to work properly, you need a block with redstone on it adjacent to the pipe. The gate won't power the pipe directly, for some reason, so you need the block, and without the redstone, some derpiness will happen when the world loads. I haven't tested this personally, though.