My method was to stick each side down onto an L shaped piece of scrap PCB. So that you can remove parallax errors between the layers and get much better registration.

Use two points on the pcb as reference points, drill, and align each separately. Hold both pieces up to the light, get both aligned, and staple or tape end of sheets together so it folds like a notebook. This requires an extra two inches or so on the end to allow flexing around the end of the board. Sometimes I also tape it to the board to keep it aligned.

Include a couple registration marks, or use some vias or through-holes for alignment. Attach one side, drill the holes, then use those holes to align the other side.