Most people like tuners aligned so that the shafts are perpendicular to the neck of the bass - pointing straight out. A few people align them to be perpendicular to the edges of the peghead.. I've seen that more on jazz guitars like D'Angelicos but it seems to have gone out of style. I find drafting tools like a clear T-square and a C-Thru B-70 ruler to be really helpful, but just about any narrow or transparent straight edge is better than nothing - there's no downside to being careful.
(click "rulers', keep clicking down till you hit the 2x12" B-70. I have those and some 1x6" B-50's, I used to give them away as useful X-mas presents....)
Masking tape also works well for making a temporary straight edge. You can measure the front and back of the tuner gear housing and be sure that it is aligned correctly. If you are drilling through finish, it is recommended that you put some masking tape to drill through. It keeps the finish from doing odd things because of the drill bit.
One thing I seen happen to me when I finished a neck on a Jazz copy. I used acryllic lacquer for the finish. When I had installed the gears back on and restrung the bass the lacquer had blistered/lifted from the wood in the front on one of the pegs. I'm thinking this was partially due to the pulling of the peg into the head. I just don't want this to happen on this instrument. I believe the wood was cleaned well before applying the finish.