I keep a piece of glass at hand to clamp in place of the negative carrier, and I start leveling from there. I go from there to the lens board/bezel (I modified my boards to be level-able) and then down to the baseboard. Then I check my easel. Having two separate enlargers, I swap easels and what-not between them at times, so I made sure that both of my baseboards were level...that way I can level up an easel once, and it works for every setup.
I also had to do a bit of milling and machining on the vertical pitch adjustments on both of my 23C's...but everything's in perfect alignment, now. I also expose at small apertures and use glass carriers, so sharpness is never a problem for me. I also don't make very big prints, though.
I recheck, periodically, as well. No adjustments yet, though.
Edit: +2 on checking with a grain focuser.
Do you ever get Newton's rings(?) from the glass, or is it a special glass that is used? Is it effective vs. glassless carriers?