Great thread.. I was wondering the same thing. Since I started vaping I have only once completely drained a battery. Im not a very heavy user (1 to 1 1/2 ml a day) so every morning I attach a fresh battery and charge the previous days battery. I try to evenly rotate them.
You have great intuition. Rotating your batteries evenly is the way to go.
Most mods (except mechanicals) will shut down when the battery reaches 3.2 ~ 3.1 volts.
Li-ion batteries, like the ones we use to vape cannot be discharge to 0 volts... If that happens the battery is destroyed and will become dangerous if you try to charge them.... This is called over-discharging.
The battery we use should never be discharge under 2.9ish volts... actually if you notice your battery under 3 volts that should be a red flag to you, you are doing something wrong.
In a nutshell.... Keep an eye on these to factors:
1 - Over 4.2 volts = you over-charged the battery and that is dangerous
2 - Under 3 volts = you over-discharged the battery and that can be even more dangerous.
When you buy batteries look at the tech sheet... This info is usually disclosed.