The orchard will automatically pick the apples (they won't even fall to the ground in an orchard, they get picked from the trees directly).
Since it is a manual farm however, it won't auto-convert the trees to Forestry's apple oaks for you though. Therefore I recommend that you start the farm up as a managed arboretum (that's the default setting without any circuit borads in it), give it some dirt, fertilizer, power and saplings. It will lay down some humus and plant the saplings there, converting them in the process. Once you have enough saplings converted thus, cut power to the farm (it might continue to work a few more blocks, as it has an internal buffer) and just dig up all the humus. You want to replace it with regular dirt for your manual orchard, and it also lets you pick up all the converted apple oak saplings.
Then you just need to prepare an intricate ciruit board with four copper electron tubes (make sure you choose the right mode on the soldering iron) and put it into the farm. Lay down dirt, grab some bonemeal and grow lots of trees. As long as the tree trunk is standing in the orchard's work area, all its leaves will be harvested, even if they hang outside of the area. So try to get a continuous canopy of leaves across the entire farm area.
Note that since the trees are all freshly grown, the orchard may start very slowly when you turn it on, and only speed up over time as more fruit matures.