I use a large mirror that fits in place of the negative carrier and remove the enlarging lens to align the negative stage to the baseboard.
Sometimes I will take a smaller mirror and place it in the negative carrier and double check that it is still aligned.
I align it with the head fairly close to the baseboard and then repeat it with the head extended fully. I double check with the head lowered as well.

Then I remove the mirror and tape a mirror to the inside of a lens board so I can repeat the process with the lens stage.
I don't print wide open. I don't even print larger than 11x14. I don't trust bubble levels, at least not the ones I own. Using a laser is more precise, simple and quick for me at least. It's very visual, you just get the dot to reflect back into the laser diode.