the saplings are fed from the top, humus from the side, the arboretum will eject sand from the side aswell. I have an iron pipe where the sand should come out, and a wooden pipe from the autocrafting table as an input to the arboretum on the other side. it is quite random which side it outputs the sand. I don't like randomness, which is why I'm not too fond of buildcraft pipes. will redpower tubes connect directly to the arboretum? both input and output?
Redpower pipes will only input to a arboretum, and it will only input a valid item as well
so what you can do is use a redpower tube circle that goes past the arboretum first. (side then top, then it swings past it and connects to a buffer attached to the other side of it, then over to a buffer connected to any side of the logger. then loop it back to the buffer chest(make certain that it is either restricted, or has more pipes than between the logger and arboretum topside. the saplings should prefer to enter the arboretum automatically, and only when that is full should they pass all the way back to the chest. use a restriction tube if needed to ensure this behavior.
Use a filter to pull items out of the item chest, and set it to pull a full stack every 5 minutes or so. excess humus will be sent back to the buffer chest when it finds that there isn't enough room in the arboretum for all of it.
you can manage the items in the buffer chest with the more expensive manager to ensure ample supply of humus, and to pull out any excess saplings, apples and the sand.
ugh. the 1.4.6 version puts the items into any of the 3 slots regardless of side nowadays, so this design is actually broken... dunno how to put the items into the right slots anymore now.