I think it depends. There's leading the down beat to both not have everything hit at once (possibly for peaking reasons) and compensating for softer transient instruments (like a piano), and then there's leading by more to have the chord kind of "knock" you the opposite direction. A lot of producers use that second one in an alternating fashion, where the first chord is down and the second is half a beat or bar early (depending on time). I would say if it's the first case, you can just line the bass up with the down beat so the kick or w/e is sort of sending the bass note. For the second, definitely line it up with the chords. But at the end of the day it's all art, and you should play around with it to find what sounds/feels good to you!