I usually run the battery down at the first use till the phone automatically shutoff. I do not know why I do that, but I read somewhere a long time ago (battery university?) while the Li-ion batteries do not have a memory effect (I know that much), the initial conditioning is preferable. So, I do so. But I also know that running down Li-ion batteries completely dry is detrimental to the battery. But the phone automatically shutting down due to low charge is not the same. It just means that the phone's protection circuit is working.
But I rarely do the thing after that. The only reason I ran down the battery, say, below 50%, is to reset its internal circuit to indicate the accurate battery charge reading. Sometimes, even after the over night charge etc, I see the charge did not reach 100%, or other odd showing (but it's rare). When this happens, after running it down a bit (say, 50%) and back it up to 100%, the problem is gone.