My trick is using a short length of hardwood about the same thickness as the surface to be hinged, the same length, and about 1/2" wide. Mark the hinge locations on it, then using a press, drill guide holes in it. Hold it to the edge of the surface, and drill the holes. Next, hold it against the other part to be hinged and drill that side.

Wow. All holes aligned properly, and no fuss, no bother.

Enjoy.

Bill.

PS: When building I drill both sides at once, if either side is built up. With solid surfaces I use the home made guide there also. wr.