You will find a laser system is much easier to use than levels. It also only takes a send to verify that things are still in alignment with the laser, so you will test it more often.
I made my laser aligner out a piece of mirror (from the hardware store glass section, no frame) and an air pistol laser scope because it had a flat side and was adjustable. The trick is to make sure the laser beam is perpendicular to the base; this is easily done with a mirror on the negative stage. If you rotate the laser and the reflected spot stays put then you are aligned. If the spot rotates around the laser you need to adjust. Once that's done you just need to adjust the lens stage so the spot reflects back on the beam. Do this again with the negative stage and you are done. On the Omegas I've used you also need to make sure the negative stage is still flat, so make sure the mirror doesn't rock at all.
The scope I used is not longer available, but a laser bore sighter should also work well, as long as it's adjustable (most are). http://www.amazon.com/UTAC-7-62-Lase...er+boresighter