I apply to both sides with a faint layer.
Two reasons I do this. First because Harc-Pro insisted (HRC instructions), and secondly because it's a good way of knowing that both surfaces are spotlessly clean and free from grease/oil etc that may stop the cases from sealing properly.
1207B cures slowly so I'll do the bottom case first, then grease the dowels and pop them in, followed by the crank. Then apply sealant to the top half and drop that on. Press it down by hand to make sure the crank seals and what have you are all lined up properly. Then gently pull the cases together with the M8 bolts, starting with the middle two. Tightening in a couple of steps up to final torque. At each stage of tightening I give the bolt heads a crack with the mallet which helps centre the crank so that the main bearings are under no axial stress.