There's a lot of myth and folklore surrounding charging iOS devices (or actually any device that uses Lithium technology batteries). A lot of it comes from the advice given for older technologies, such as Nickel-Cadmium or Nickel-Metal-Hydride batteries. None of this applies to Lithium, however, and some of what we "know" from the NiCd and NiMH days is actually harmful to modern battery technology.
Things to understand:
The "charger" for an iOS device is built into the device. It is not the thingy that plugs into the wall, and it is not the cable that connects the thingy that plugs into the wall to the phone. They are just a source of current and a way to get it to the phone, respectively.Completely draining a Lithium battery, even once, will kill it. (Unlike NiCd and NiMH, which people really would drain completely to prevent "memory effect").The internal charger is "smart" - It will prevent the device from being overcharged, and it will attempt to prevent the device from totally draining the battery by shutting down the device before the battery is fully depleted.When the phone shuts off at 0% it really isn't zero; there's still sufficient charge on the device to prevent the battery from going completely flat. Likewise, 100% is not the maximum the battery can store; it stops charging slightly short of maximum to prevent overcharging.The worst thing you can do is drain the battery to 0%, then not charge it immediately. After it reaches zero and shuts off there's a small amount of energy left, but if you leave it uncharged for long it WILL go flat and kill the battery. So if it reaches zero, charge it soon (within hours). And never leave a phone unused for weeks or months on end without periodically recharging it.You should only use high quality USB power sources to charge your iOS device. They don't have to be Apple's (although Apple makes good ones), but they should never be cheapo USB sources, both because they may damage the phone and they may even injure you.The power source needs to supply at least 1 amp to charge an iPhone, and 2 amps to charge an iPad. Note, however that a power source that can supply more than these values is OK to use; the internal battery charger will take only what it needs. So, for example, you can safely charge your iPhone with an iPad USB adapter.iOS devices fast charge until they reach about 75%; the rate then slows down to prevent overcharging. So it will reach 75% very quickly (under an hour), but it can take a couple of hours more to reach full charge.
So what are the "rules" for charging? The most basic one is charge whenever you want to, for a long as you want to. There's no reason to let the device drain completely before charging (in fact, it's a bad idea to do that on a regular basis), and there's no need to wait until it reaches 100% before removing it from the power source.  You can charge when it's at 40% and disconnect when it reaches 80%, or any other values, without hurting the phone.
The Best Practice, however, is to charge the phone overnight, every night. As it stops automatically at 100% you can't overcharge it doing this. You thus start the day with a fully charged phone. And, if you configure the phone for automatic backup using iTunes or iCloud, the phone will back up every night when it has a WiFi connection and is asleep. Show all