So i'm trying to get ancient warfare to automate my furnaces. So i want some of the furnaces to produce charcoal. However whenever the courier comes and takes the charcoal from the output slot (The "down" inventory) he also takes all the charcoal from the fuel slot (N/W/S/E inventory). It appears the "down" inventory includes both the fuel slot and the output slot.

I work my way around that by just placing Logs in the Fuel and INPUT, and just taking charcoal out of the bottom

That is the vanilla furnace implementation. Just don't use the "down" inventory for those.