There are sooo many misconceptions about todays cell phone batteries. The whole 'cycle through from full to empty a half dozen times to optimize the battery' thing is a carry-over from older style cellphone batteries. That doesn't apply to todays Li-ion batteries. If you want to just for the sake of making yourself feel better about it (like I do), that's fine, but it really doesn't make any difference.
Likewise, when you run your phone down until it shuts off, you haven't completely drained the battery. Your cellphone is designed to shut itself off well before the battery is actually dead in order to protect the battery. So you really don't need to worry about doing that either. However, if you want to throw it on the charger when it reaches 40% then go ahead, it won't hurt it either.
Basically, there's not much you can do to screw your battery up. We're all just used to older style batteries that were finicky as hell.