My process has been to secure stock however is convenient and mill two tight fitting pin bores that match the pin holes on my waste board.
I use mcmaster brass dowel pins for this so they are more robust than the wood, but soft enough for a mistake to not be a disaster. I also rather have a press fit to avoid any slop that could affect alignment later on. A free fit means clearance, which means misalignment later. So far, I’ve been able to pull the pins easily enough with pliers.
I then flip onto those first holes with pins and zero the piece X, Y, and Z for side one. During side one I mill the holes for the flip, tight as before. I flip the part onto the same pin holes in the waste board and only rezero my Z. I then mill side 2.
I’ve been able to manage 4 side milling with this method.