I don't think it really matters where you start so long as you make your final decision based upon your ears. I would typically start with the pickups where they are when the bass comes to me, unless maybe they are extremely low, high, or tilted, and adjust from there. Typically I am going to tilt the pickup if I hear that the low strings are too loud compared to the high strings or vice versa, and for me this varies by every single bass. I am not usually all that concerned with output, so the question of how close the pickups should be to the strings is based primarily on whatever I think sounds best and again will vary from bass to bass and pickup to pickup.
I don't have any answer for the question of "how much bottom end is enough" other than to use your ear to decide whether the bottom end is good for you, which is going to differ for every person, and even with the same person they may have different preferences depending on the sound they want from a particular bass. I personally probably go for a little bit less bottom end than the average bassist because for my playing and tone I find that if the sound is too bass heavy it tends to cause the low notes on the bass to be too dominant and make playing in the middle and upper registers sound a bit weaker. Particularly thinking from a live and recording perspective I am trying to set up a bass to sound as good and even as possible across everything I will be doing.
