UNDERSTANDING DISCHARGE LIMITS
It was pointed out before that your LiPo cells are nominally rated at 3.7 volts per cell. When they're finished charging they will actually be at 4.2 volts per cell. As the cells discharge during use the voltage being produced will quickly go down from the 4.2 value and remain fairly steady in the range of 3.75 to 3.8 volts per cell. Under a heavy load they will drop as much as .3 to .5 volts but when relieved of that load they will return to and remain at approximately 3.7 volts until almost fully discharged. It is, therefore, this voltage level that represents the rating of the battery.
You may be asking (as a true LiPo Ninja would), how do you determine when a battery is depleted and it's time to land the helicopter? There are a few rules of thumb to determine how much of the battery's capacity can be used safely. One rule of thumb says to not use more than 80% of the battery's capacity. To know if you've gone beyond 80%, it helps to have a charger than can keep track of how much capacity (Total mah) was put back into the pack during the charge cycle. Divide the mah put back into the pack by the rated capacity of the pack (and then multiple by 100) to determine the % that you used and try not to exceed 80%. If you are keeping track of how much time you're flying and how much mah is being returned to the pack with each charge it isn't hard to come up with time guidelines that will keep you from exceeding the 80% discharge rule of thumb.
Another rule of thumb (the one I prefer) is to not let your cells go below 3.3 volts. There are inexpensive and very lightweight battery monitors/alarms that plug into the battery balancing tap/plug and that can be velcroed to the side of the battery. They are generally set to alarm when any one cell in a pack goes below 3.3 volts. The alarms may activate if you quickly increase throttle causing the voltage to sag but if they stop when your reduce throttle then you're generally safe to continue. A continuous beeping alarm during normal hovering flight indicates it's time to end your flight (preferably with a nice landing). Again referring to the information provided by a good computer controlled balancing charger, it's possible to see exactly what the individual cell voltages are in the pack when it's hooked up for charging. This is a good opportunity to decide if it's safe to extend your flight times a little or if they actually need to be shortened.
It's important to know that the cells in your LiPo packs must be kept between a range of 3.3 volts and 4.2 volts.
The upper limit is managed by your battery charger in that it should stop the charge cycle when 4.2 volts per cell is reached. It is up to you though to keep from discharging your batteries below the lower 3.3 volt limit. Multi-rotor helicopters are unique in that we don't generally use any voltage protection features within our ESC's to protect the batteries from low voltage damage. If we did, we'd have helicopters falling out of the sky as the ESC's tried to protect the batteries by shutting down the motors. Some flight control systems have methods to alert you of low voltage condition. Consult your user manual or online wiki for more info.
PROPER CHARGE LIMITS
There's another detail on the battery label that is important to understand and it too is listed with a capital C. It indicates the limit at which you can charge the battery. Modern LiPo balance chargers will usually auto-detect the voltage of the pack and will choose an appropriate voltage setting for the charge cycle. It's up to you though to select the amount of current that will be applied to the pack during the charge cycle and this will determine how quickly the pack will finish charging. The capital C again stands for capacity (mah of the pack). To understand this let's look at a 4S pack with a capacity of 5000mah and a max charge rating of 2C. THe 2C rating indicates that the pack can be charged at a rate of two times the capacity. Divide the capacity of 5000 mah by 1000 to get 5 and then multiple it by 2C. The maximum current (aka amperage, aka amps) setting you can use on the charger is 10 amps. Some batteries may be rated as high as 15C but keep in mind that charging at maximum rates will likely reduce the life of the battery. A ten minute charge may sound nice but it will likley shorten your battery's life which isn't so nice.
Also regarding chargers and charging, there are a lot of chargers that advertise the ability to charge multiple batteries simultaneously using what is called "parallel charging". This means that groups of packs are connected to each other and to the charger in order to be charged (as far as the charger can tell) as one large battery pack. It should go without saying that if you don't fully understand how to charge one pack at a time then please don't attempt to parallel charge multiple battery packs.
A significant danger involved with parallel charging occurs when packs are connected together where one pack has significantly more charge remaining than the other packs. What happens is that the greater voltage in the less-discharged pack will cause current to flow into the more discharged pack with the lower voltage. To put it another way, the higher voltage pack will act like a battery charger on the lower voltage pack! The problem is that this happens very quickly and without any control so it has the potential to start a fire. The rule of thumb for parallel charging is that the individual cells within the packs should all be within .1 volts of each other prior to being connected to the charger. This means all of the batteries being connected need to be at a similar state of discharge.
Why balance charge anyway you might ask? In the early days of LiPo batteries, it was common to charge the packs like any other battery pack by connecting the charger to the power plug and charging it as if it were one big battery cell. It wasn't that this didn't work, it's just that when one cell within a pack became out of balance with the other cells in the pack, it created the potential for the pack to overheat and catch fire. There are many stories on the internet of people that connected their chargers to their car battery, started a charge cycle and walked away only to find a few minutes later that their battery had caught fire along with their car! Houses, workshops, cars.....they've all been lost to LiPo fires that started during battery charging.
It didn't take too long for the LiPo manufacturing and using community to realize it was important to monitor the individual cells during the charge cycle and to control/charge them as individual cells. When you charge a four cell pack with a balancing charger it is actually running four charge circuits (one for each cell) and speeding up or slowing down the charging cycle for each cell as they lead or lag each other. If one cell takes a charge more quickly and its voltage begins to exceed the voltages of the other cells in the pack, your balancing charger will slow it down so as to keep it at a similar voltage as the other cells. It is "balancing" the voltages of the individual cells as the pack is being charged! Get it? The potential for batteries to catch fire during charging is always there so please only charge your batteries on a non-flammable surface like cement, outdoors if you can, and try not to leave your charger unattended while charging.
If you've come to LiPo batteries after having used NiCad or NiMh packs you may have wondered what that extra set of wires coming off of the battery was. The extra wires are connected to the balancing plug and the wires/plug together are commonly referred to as the balancing "tap". Some chargers will charge only through the balancing tap, others will charge through the main power wires but also through the tap for control of the process. There are charging guides that say it is safe to balance charge every ten or twenty charges but, in my humble opinion, if you have a balance charger, use it every time you charge your batteries.
Internal resistance is yet another concept that relates to the overall health of your LiPo battery packs. Even a simple length of copper wire has a certain amount of resistance in it. Resistance (measured in Ohms) is the characteristic of an electrical circuit that prevents electricity from flowing. It won't necessarily stop the flow of electrons but it will just make it harder for them to flow. Make it too hard for the electrons to flow and the current passing through the wire will produce heat. Make too much heat and we're back talking about, you guessed it, fire. High resistance in your batteries will make them run hot for a little while and there will be some signs things aren't good before they think about catching fire but if you ignore the warning signs completely a fire may be just around the corner.
Chances are if your battery packs aren't delivering the same power they used to, resistance is building inside the packs and it may be time to considering disposing of them. Other warning signs would include packs that are hotter than usual after use and puffing which is what it's called when your normally flat and tightly packed LiPo battery begins to take on a more inflated and rotund appearance. Slight puffing isn't the end of the world but a LiPo Ninja would take it as a sign to watch things more closely and to monitor/measure the cells' internal resistance on a more regular basis.
Here's a video on how to measure internal resistance
The video demonstrates a procedure for a 3S pack so you'll have to modify the procedure if you're using packs with different cell counts. If you're checking your packs on a regular basis, logging the values on the cells will help you to see when the values begin to increase indicating the pack is aging and isn't as happy as it once was.
Some advanced chargers will be able to display the internal resistance of the cells. Refer to your user manual to find out of your charger has this feature.