So saplings into the orange and black space, and I can have a side pipe on whichever color that will deal with any overflow that might accumulate? Also, all sapling go straight to the planters, so is it best to wait for them to fill up and siphon off the overflow or... By Redpower tubes, do you mean pneumatic tubes? Kind of confused on that part.
Yes, pneumatic tubes are from Redpower. Generally whenever someone says "tube" they mean those and when they say "pipe" they mean the Buildcraft ones. But not everyone gets the distinction right all the time.
As for the diamond pipe, just make saplings go down the black path. If you mark them for both black and yellow, the pipe will split them 50/50 between those exits, and we don't want that because we want as many of them as possible to go into the juice Fermenter so that the juice gets used with priority. But if you mark
only black, then it will force all of them to go down that route. And then comes a neat trick: a Buildcraft pipe directly attached to an inventory (such as the Fermenter) will allow an item to try an alternate path if that inventory is full, instead of spilling it instantly. The alternate path must be different from the path the item arrived from (green).
Basically, all saplings are forced into the first Fermenter all the time. But if that fills up, then the saplings are allowed to try for a different exit of the diamond pipe if one is available. They cannot go back the way they came through the green exit, because that is forbidden by default, so they choose the only option remaining to them: the way forward to the second fermenter, through the yellow exit. No need to set the filter for yellow at all (in fact, setting filters can sometimes break this behavior so better don't).
If you want to deal with overflow on the second Fermenter, again use a diamond pipe that filters saplings down the black exit, and then attach an alternative route so they can travel on if the black exit is congested.
Tubes simplify this because tubes never overflow (they send the item back to the source instead, which becomes "backstuffed" and waits for room to free up before sending more) and always fill the closest eligible inventory first. That means simply attaching a bog standard pneumatic tube to the top of the two Fermenters takes care of all the item navigation automatically.
I don't know anything about MFR planters, I'm afraid, but while using Forestry farms I always let the farm fill up on saplings and eject the overflow. That's the default behavior for the new Forestry multifarms anyway.