Well...how to do it and best setup are all relative. I can tell you how I do it. I use a farm to make wheat, The wheat is sent into a chest and an autocrafting table combines it with dirt to make compost. The compost is the catalyst to make biomass. The Farmer and Combine do not need anything really but MJ and seed/dirt to run. But you should look to alternate methods as 1.5.2 and the latest forestry will remove those items.
To get the Sugarcane, I use a Sugarcane harvester, if I have space for it I plant a couple 21x21 fields...or I can use two fields carefully stacked per harvester. Sugarcane is a weed and grows very fast. After that the cane and compost go into a fermenter. Cane will enter from the top while compost enters from the bottom. Power and water/juice can come in from any where. All you need to do then is suck out the Biomass.
As a special note, I prefer to use Liquiducts to transport fluids, they are less of a logistical nightmare. But I have used waterproof pipes also. Once you have your Biomass, you can pump it into a tank or send it to stills for processing into biofuel. To save on pipes, I use combustion engines...one attached to each still. They provide plenty of MJ and the still fuels them with plenty to spare. Just make sure they have enough water or BOOM!. Pump in Biomass, prime one engine, fill the other engines (One Fermenter can produce enough to run four stills if set up right) with the biofuel then off it goes.
The biggest issue if getting enough cane or saplings depending on your bent into the system as the fermenter at full power will blow through a stack of cane in about 90 seconds. I have my cane barrel and compost chest attached to Red Power filters and those on timers so when each thing runs out the timer will pulse and the filter will send out a stack. You should do stacks or half stacks if you use a timer as pulsing one cane every 1.2 seconds can cause ALLOT of lag.