Could you etch one side, drill it, and then line up the holes. You would have to tape over the side not being etched with packaging tape. I have taped over a side that I was not etching, but didn't remove the tape.
I cut the layouts a bit larger than necesary and than stick (with tape) one layout on a spare piece of PCB.
Align it in such a way that it is a stop for the PCB you want to make.
Turn it and align the second layout before taping it on to the spare PCB again. I use additional lines, on every corner of the PCB, in my layout, for alignment.
You got a sandwich like layout wherein between you can put your PCB. Then before exposure, also tape pieces of the layout to the newly to be exposed PCB. Now it is stable enough to turn it after the first exposure.
Add two reference hole to your design (e.g. in each corner).Then, print one of your layers on a regular paper sheet. Drill the two reference holes using this sheet. After it is very easy to align each side using these holes (expose each side then develop).
If you're using presentitized boards and if you drill before etching, you'll realize that the photoresist will chip around the hole...then you'll lose your pad. (This is what happened to me)