Lithium batteries do not have a memory effect, like NiCads. You can charge them any time you feel like it.
When people say a battery will be good for 500 cycles it means that the battery will hold 80% of it's original charge.
A cycle is from discharged go fully charged so, for example, if you charge it up when it gets to be half empty you can charge it 1000 times.
A battery will read about 4.2 when it is full. When you start to use it it quickly falls off to the mid 3s and then goes in to a long gradual decline, when you spend most of your vaping tine. As it nears the end it again falls rapidly to under 3 volts, you can usually tell this point cause it is the "Why am I not getting as much vapor?" point.
At some point under about 3 volts you start to hurt your battery. Using it at a low voltage will give bad vapor and shorten the life of the battery. Nothing horrible, explode ot burst into flames, will happen except you will have to buy a battery sooner.