I posted some pics in another thread with my design
http://forum.feed-the-beast.com/threads/efficient-eu-production.2387/page-2 , but I'll have a go at explaining the setup.
Basement with routing excess items to chests, 2 x carpenters for bog earth and humus. Also contains a mulching room, biomass and seed oil tanks with production and everything powered by biomass engines. Wood goes to another plant next door, producing charcoal and creosote, charcoal then heading to generators turning it into IC2 energy.
1st floor has the peat farm, 2nd and 3rd are wheat farms and top floor for the tree farm. All the engines here are peat powered with overflow chests for the mats needed. Once the main chests are full, the overflow chests pump materials (seeds, saplings, spare peat) down to the basement for sorting and processing. All this can be done through the building 'core' and if you leave a 3 block gap, then add a 3 deep layer of glowstone over the wheat, you have enough light for 24hr growth. Requires a lot of resources (d-pipes are essential) but if you set it up right, you can have 1 main pipe running through the building with almost everything going through it, the exception being the peat for engines.
An alternative would be to splash out on a hybrid solar panel and MFU, placing it dead central and 3 blocks above the arboretum, then running wire to electrical engines, replacing the peat ones which would save a lot of space and pipes, as well as getting rid of the pesky ash... The system can keep 9 coke ovens full in the charcoal/creosote plant (although i've added a second tree farm on that building, bumping it to 24 ovens-which turned out to be a little overkill, lol) with wood to spare.
Outputs wood, apples, excess wheat, excess mulch, seed oil and biomass with, if you add on the coke ovens, creosote and EU from burning charcoal and peat.