I take it from your post your a bit of a novice & thats not a bad thing btw, I will try to outline a simple setup for you.
first off I take it, its the multi block forestry tree farm or a steve's cart, as multi farm is a little newer I will try cover that one, you should go to the forestry wiki & check out the requirements, first the farm blocks needed plus valve, gearbox, & two hatches are all needed the controller can be done with out for now, now the for bricks, use stone brick as its easy & fast to make from spare cobble, by this time you should have read the required multi block info & have a fair idea of how to set a farm, I find it best to built its level with the ground, when you have you 3x3x4 or what ever you pick in place it will change into a multi block farm you can see this by the band around it, now we need to lay out the brick for the farm to plant on, again follow the info on the forestry wiki but my advice is to dig down 2 blocks & place the brick at that lvl so the finished soil level will be level with the ground, now to autiomation of this part, its really not that hard as the hatches use gravity to import & export items if setup correctly, take 6 stacks of ditrt & fill the top left slot, add any valid sapling to the top right, the bottom to sections are the output, now to semi-automate fertilizer try this on the top face of the multi farm remove a farm block & replace with a hatch block on top of this put a vanilla hopper & on top of that a chest, fill the chest with fertilizer & the farm depending on size of farm & chest will run for days or weeks.
I forgot to mention the circuits, there are 2 types you will need the automated intricate one (managed arboretum) with 4 copper tubes, for this you will need a soldering iron, hold the soldering iron & clicking will bring up its gui, do not add the circuit untill you have selected managed farm & placed the 4 copper tubes in place, after your sure you have it correct add the circuit, the finished circuit is added to the farm in the slot on the left matching the shape.
now we need to get the excess sapling to turn them into biomass, I tend to do most all this machine setup under the farm its self for easy of use & for safety (it really hurts when a cheeper comes creeping) you will first need to hook up water to feed the farm, the easy way is a TE aquarius accumulator, you can use bc water prof pipes or liquiducts to fill the farm in normal biomes 1 AA is enough but in hotter more will be required, next is some form of bc power to start one Stirling or any other engine will get you started, I use TE steam hooked to the same AA & some charcoal from the excess wood, you can also turn the wood into planks & burn them in the engine, you need a gearbox on the under side of the farm this you power with conduits as then are self buffering & help regulate the engines & you have less power loss, now we are ready to add the second hatch & remove the excess saplings add the second hatch some place on the under side of the farm make sure you have clear access on 3 sides, you may wish to add a diamond pipe to the hatch so you can sort the apples/wood/sapling out, send the apples too a barrel at least 8 blocks away, we will use the apples later, this is what I like to do with the wood to make the farm self supporting & the reason I use TE steam engines, make from 2-6 engines & hook them up to the water pipes on one side not under them, over each engine drop a TE furnace & set the output to bottom & input to top, pipe wood into top, this way the furnace will feed & buffer charcoal to the engines, now add your power conduits, now we have a multi farm that can support its self & is semi automated fertilizer, the power from the engines will power the farm & the fermenter/s to form the next step in the chain.
now step back & think about the layout of the next part & if you wish to store biomass or convert to biofuel asap, if you intend storage you must allow room for tanks there are 3 types normally used the stanard BC galss, the RC multi block iron tanks or the xy craft multi block, this I will leave to you to work out but I would advise not making huge tanks as liquids can be the result in lag, so lets say no tanks we will process all first & then if required store teh end product, so dig out a new room off from the farm room, now we need a fermenter or two, place a fermenter conected a water a pipe & power,(yes I know apple we will get to that later) over the fermenter at least 2 blocks above place a barrel, pipe the sapling into the top of barrel, this will be the buffer to stop any overflow, now make some red pipe wire & one Iron and one antarctic gate in an assembler, on the bottom of the barrel place a wooden pipe & any other pipes down to the fermenter click the pipes with the red pipe wire, place the antarctic on the wooden pipe set it to red pipe wire signal on - engine on, on the pipe touching the fermenter place the iron & gate set to resource 25% - red pipe wire signal, this will keep the fermenter working, the boimass can be piped directly into a still & turned into biofuel, this then can be used in boilers or on some engines, as a side note I normally add a chest & 2 more gates to keep the fermenter full of firtilizer/mulch.
I have typed this from memory if I made any minor mistakes I will fix in an edit later, I will add a part 2 tomorrow.