It would work with this.
W S
L I S S S
L is logger, w is wooden pipe, S is stone/cobble/gold pipe, and I is an iron.
I have it like this:
I S
L S S S S
You don't need a wooden pipe, the Logger, and I think all other Forestry planters/harvesters, outputs its stuff without the need for wooden pipes. The iron pipe prevents stuff from leaking out of the pipe if it tries to go there. The one on the side can be a regular pipe because the Logger doesn't accept any items, it only outputs.
I also run Additional Buildcraft Objects (ABO), so I actually have it like this:
S
S In S C
S = stone/cobble/whatever pipe; In = Insertion Pipe (from ABO); C = chest.
The Logger is behind the left S; the Arboratum is behind the In; behind the top S is an iron pipe (on top of the Logger).
I could optimize it a bit by moving the Iron pipe to the side of the Logger, it will still do the same function, except items will be turned back sooner.
