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.
http://www.cthruruler.com/
(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....)