I have a few steps I take for each board before I start the actual drilling, plating, etcing process.
Mark the board with the project name and board version.
Drill an alignment hole for resetting zero on the mill.
Since I tent to work on several different electronics projects at the same time I like to engrave the project name and board version number on the board. This helps me keep track. If you're only working on one board at a time you can skip this step.
I also drill a small alignment hole 0.010 inches on the negative X axis. If for some reason my mill gets out of zero I can use this hole to re-located the zero point. I also use it to check the board for being in alignmnet if I have doubt.s It really saveve me from spoiling a board sometimes.