PCBgogo

I'm learning the photo resist method, and early signs tell me it's the way to go. Just way fewer ways to screw up. Different ways, but still fewer. 
Anyway, I'm not certain what the best way to align my transparencies for a double sided board.
I've seen video of folks taping one end together, but that seems like it would still allow movement. In fact, to me, if you taped two sheets together, and tried to slip a board between them, they'd have to offset to accommodate the board.
I have tried 3/16" fiducials with cross hairs in them, and using a third print as a tool to drill these holes into the board, so I can use the holes to align my sheets. That seems to work, but now I'm concerned that I'm leaving the boards exposed to light too long while I'm fooling around lining things up.
I'd love to use a similar system to what the pros use, i.e., holes in every sheet and board, and rods to thread everything on to , but I can't see how to do that and have the necessary pane of glass on top of the stack.
What works well easily? Btw, I'm using my scrap component pins for vias, and will only ever connect 50 mil traces with them. In other words, I don't need amazing yet. But someday I might want more.