You can run the output of the skimmer over the side of the sump, but you leave the output pipe submerged; this way you don't have back pressure to the the height of the sump wall, only to the level of water in the sump. When you set it up, you want the level of water in the sump to be no higher than the top of the skimmer box, about 8". Sometimes this means putting the skimmer on blocks or a little stand. It's a little neater to have the skimmer output go directly to a bulkhead back into the sump rather than PVC pipe up over the edge and down into the water, but the function is basically the same.

As far as the bulkhead for the skimer pump feed, put it low in the sump, well below water level of course. Probably the exact location should be determined by the placement of your skimmer pump. My guess is you want a ball valve and union to the pump, and not much else if it fits well. Like, if your pump is going to sit on the floor next to the sump, measure the height of the intake fitting, and drill your hole the same distance from the bottom of the sump. The ball valve is for shut off only should you want to remove the pump. You can get one of those nice union/ball valve combos.