@OP: the easiest way I've found to do this is to place the farm hatch on on of the corners of the multiblock structure. This then allows you access to three of its sides: bottom and 2 of the sides.
My setup currently is to autoeject items into a diamond pipe and define in the diamond pipe GUI where specific items should go (i.e. apples to fermenters, wood to sawmills, etc.). On each side of the hatch I've hooked up an RP2 relay. I manually fill one of them (which doesn't have any pipes/tubes connected to it) with fertilizer. The other is used to pump dirt or any other soil needed into the farm.
The only thing that took some time to figure out was which side of the hatch needed to have the fertilizer. Trial and error worked fine for me since placing fertilizer in the "wrong" relay meant it was sent into the "to-be-planted" slots (i.e. the sapling slots).
As you may notice I've not (for now) automated the creation and supply of fertilizer since I've found that 9 stacks of fertilizer in the relay + 1 stack in the farm ties me over for many MC-days on end.
Hope this helps,
Bel*.