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 mil

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.