It all depends on what your goal is as to the best method.
Are you looking for dead-on squareness or are you looking for repeatability?
If it’s dead-on, you need a perfectly square machine with accurate spacers and exact belt tension and Vwheel pressure on both sides.
My biggest issue was power cycle to power cycle squareness (repeatability). I had some spindle mount holes go slightly off plane due to this among other things.
What I did was created a jig. It’s 2 pieces of left-over 20x20 extrusions from the sideboard and then I used a longer 20x20 piece with the corner gussets and tied them together.
I put that on the top every time and pull the gantry square then turn on the machine. By doing this, I know the “square” is the same every time and so I can easily do half a carve, stop for a day or so, and then come back and as long as my material didn’t move, I’m good.
I made a clamping fixture for some same-sized signs I was making. I squared the machine using my contraption, squared the fixture to the axis and then left it in place. Over the course of a month I carved 50+ signs and all I had to do was use my contraption to square the axis and they were all the same across the length of the board.
EDIT Found an old picture of my “jig” I posted in a different thread…ignore the mess.:
Another thread with some good info about this: