For double-sided milling, I have a row of evenly spaced holes across my spoilboard. When I want to do double-sided milling, I first bore two holes in the stock that match two holes in my row of holes, then put pegs in the holes to align things. This way, I don’t turn my spoilboard into Swiss cheese.
For double sided milling, I bore a hole in each corner (using estlcam). Use 1/4"steel dowel pins to locate the material. I use all four corners because I’ve had some of the scrap break off and made it impossible to line back up. There are normally at least 2 pin locations remaining to locate the material for the reverse side. One caveat, double check the actual diameter of you bit beforehand (had a set of 1/8" bits that were undersized). Keep a note pad to record the starting point from home, so you can easily rerun the same job at the same position, to minimize holes in spoilboard. Just my two cents from what works for me.
That’s a little similar to what I’m doing now, index holes are definitely part of it. I run them through the actual workpiece though so I can re-align at any point of the process. I’m planning on tying in a fixed origin and a vacuum bed on this machine, get rid of the indexing entirely (hopefully) on the build.
I’m at a standstill on the build right now, my idler pullies have disappeared into the great unknown of the shipping universe and my lead screw is apparently being walked here. But the controller arrived today, so as soon as the idlers show up I think I’m on to final assembly and wiring.