I just tried to make sure my designs lined up in the document I made. I think they were best lined up in the corner and maybe got off the tiniest bit as it went out and got further from the start point.

One way to do this that I didn't think of at the time (I was very new to laser cutters) is to etch one side, cut them out, then flip them over in the board (so the holes hold them in place) and then etch the other side.

My way worked for me, but etching, cutting, etching again might be the best way to do it.