Redstone energy conduits accept power from anything that makes MJ - basically anything that has "engine" in its name. A cheaper alternative is gold conductive pipes (gold pipe+redstone). To use conductive pipes you'll need a wooden conductive pipe taking the ouput of your engines. Note: unlike normal or waterproof wooden pipes you don't need a redstone engine to pull the power out - you just need the pipe attached to the engine you want to output power from.
Handling overflow with BC pipes means you're going to have to use diamond pipes. It's been a while since I've used it, but I believe Extra Buildcraft Pipes (I think that was the mod's name) provides an insertion pipe that would work instead, but that's not included in FTB.
The way I'm envisioning the system you'd have your harvester output into your pipe system. Those pipes then lead past your planter where you have a diamond pipe telling saplings to go into the planter. The pipes continue on from there with any saplings that can't fit in the planter and come to your fermenter system. First you'd have a diamond pipe pushing apples into a squeezer followed by a diamond pipe pushing saplings into your first fermenter ( this one is hooked up to the squeezer for apple juice). After that you'd have another diamond pipe pushing saplings into a 2nd fermenter (this one filled with water from an aqueous accumulator or something similar). Finally, you'd end with an overflow chest. Preferably something with lots of storage capacity like a diamond chest or barrel. At any point along this line you can inject a diamond pipe to pull out the logs for use elsewhere. The mulch from your squeezer could either be routed through another set of pipes with diamond pipes pushing it into the fermenters or you could use iron pipes to hook the output into the main line and add mulch to the diamond pipes pushing saplings into the fermenters. Either way, after being routed past your fermenters, the much should end up in an overflow chest. All told, you're looking at least 5 diamond pipes, but max 7 pipes. That's still less than 1 craft's worth, so you should actually have extra.