As a general procedure, level off the baseboard, l/r front/rear. Then get the neg stage to match.
Lastly get the lens stage to match the baseboard. This can be tricky because lenses are not always accurately mounted and some adjustment may be necessary. You might have a lens with axis slightly off center. All except my Leica lenses are all different.
The level does not need to be precise, just repeatable. Use the same end to the right & rear all the time. Try to do the neg stage with the head in place so weight does not distort later.
If you center the bubble, you will be very accurate towards parallel planes.
No fancy tools are necessary.
Check the f/r & l/r with a grain focuser. Then do the corners. If the image achieves better focus when you raise the focuser and the opposite can not go far enough down, then the lens itself is off some and you need to twist/shim the lens stage. Tape makes a good shim.
Omega and Peak grain magnifiers with the long mirror work right into the corners.
That is all I do and get perfect alignment. All except for the Leica enlargers because they are never off, I just check for heck of it. Omega & and Besslar just are not precision tools and you have to fight them all the way.