I've just started working on it, but what I plan to do is print a "center line" on the carrier then fuse it so it stays there. I can then either drill 2 small holes in the pcbs and line them up over the holes, or notch the top and bottom of the pcb and align the notches to the center line. The top of the pcb can fit against a "stop" epoxied to the carrier. Print one side, fix it in acetone, flip it and print the second side. Then fix the second side. Should work.
As things are now, if I print an X on the pcb then run it through the printer a second time, it usually prints right on top of the first print.
Mark
At 02:50 PM 8/3/2014, you wrote:
How do you handle registration when doing a 2-sided board?