I've only done the UV exposure method double sided. I used 4 thumbtacks, one in each corner, to align the masks.
At the time (work), I had the ability to spin coat the resist and bake in a "yellow room". The holes slightly messed up the uniformity of the resist since they were drilled prior to coating. Moving the drill press from the machine shop wasn't an easy option.
I keep mentioning that I used the surface tension of water (a drop) to keep the photographic mask against the board instead of a glass plate.