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Lipo Information

So, You either are currently using LiPo (Lithium Polymer) or are planning to use them with your RC aircraft/car?
Well, there are some important things that you need to know about using and charging these types of batteries. Lets go over the basics of safety you REALLY NEED TO KNOW!

BASICS
1) ONLY use a balance charger designed for LiPo batteries. Charging a LiPo with another type of charger WILL CAUSE  A FIRE.
2) Over discharging (charging to 5% or less capacity) will damage the LiPo and likely make it PUFF and/or not perform well for subsequent flights/uses.
3) A properly fully charged LiPo will be 4.20V per cell.  Operating a LiPo to 3.0V or less under load (no matter what the capacity) can damage the battery.
4) Puncturing the outer foil casing around the battery cell renders the battery into an unusable and often dangerous condition that can cause smoke, heat and/or fire.
5) Operating a LiPo above 160F will damage the battery. If it's too hot to touch and hold onto, that's about 140F and likely, your over taxing the battery.
6) Lipos don't perform as well when too cold or too hot. Room temperature is a about a good average temperature where Lipos perform well.

Break-in Procedure
There are a number of procedures people follow. If the manufacturer has a procedure that is recommended, you should do that.  But here is what I do (Assuming a 6-8 minute calculated run time):
Start with a complete Balance Charge (Lipos are typically shipped half charged [storage voltage])
Flight #1) 2 minute at 1/2 throttle (for a helicopter, simple hover), Then Balance Charge.
Flight #2-4) 2 minute at 1/2 throttle, Stop for 2 minutes, 2 minute at half throttle, Then Balance Charge
Flight #5-#8) I take it easy, not hard flying and target discharging about 70%

Setting the Timer for your flight
Target your timer so you do not exceed 80% discharge. No better way to degrade a battery than to overdischarge.  If you set your timer for 80% discharge, then you know you have enough time to deal with special circumstances after the timer goes off. Start slowly and keep increasing your timer until your flying and you know how long say 75% discharged is.  If you hit the timer and you've been taking it easy, maybe fly longer, if not, land when the timer goes off.  For a Helicopter, I set the timer about 1.5 minutes less than how long I can hover and get an 80% discharge. How long your battery lasts depends on how hard your working the throttle. (same goes for Helicopters, more 3D and hard flying, the less the battery lasts). A timer will work if your flying is consistant and you are monitoring how much mAh your putting back into your battery.  A hard flight? End it early. Taking it easy? Maybe consider adding a minute to your flight?

Connecting in Series
Yes, you can connect batteries in Series and run them. Many people do this.  You want to buy or make a series harness so you can keep and charge the batteries individually.  I recommend (and many other people do) that when you run 2 batteries in series, that they be the same brand, C rating and Capacity and age/use. They don't need to be the same size though. For example, I often run 2 3S 2200mAh 20C packs in series in a combat plane to make a 20C 6S 2200mAh pack.  You can also run say a 2S 2200mAh 20C in series with a 3S 2200mAh 20C pack to make a 5S 2200 20C pack.  Some people do this because 2 and 3 Cell packs are easier to acquire.  Or they do it because for my case, I have LOTS of 3S pairs hanging around from Helicopters and I sized an Airplane motor to work on 6S 2200.  If you DON"T make sure the capacity and C ratings match, what can happen is one battery pack may drop more voltage under load (See Internal resistance below). This may not be seen by your ESC battery monitor, but that pack may end up puffing or discharge more than the other pack.  If you have access to a charger that can measure Internal resistance, it would be a good idea to matcht he batteries to similar IR values (withn 30% of each other). The shorter the runtime of the aircraft and the harder you are going to push the battery, the more critical this becomes.  (Read section on Parallel charging).

Connecting in Parallel
You can connect batteries of the same Cell count in parallel and run them.  When connecting in parallel, you can get away with different capacities and C ratings.  You don't want to get too carried away with the difference but what will happen is that most of the power will come from the higher C rated pack (or the higher capacity pack) and less from the lower C rated (or lower capacity pack). Some cross charging will occur when the motor is not running but in general will be fine.  Connecting in parallel is less common but some people do it when they don't have a large enough capacity pack.  2 3S 2200mAh 20C packs in parallel make a 3S 4400mAh 20C pack. In general, it's best if the larger capacity pack has the higher C rating. Before parallel connecting packs, you should seek advice from a forum to see if what your doing is ok.   Paralleling a 3S 2200mAh 20C pack and a 3S 500mAh 30C pack may not be the best idea.

Charging in Parallel
You can charge batteries in Parallel. You should always do this with a parallel Charge harness and a Parallel balance harness. DO NOT charge without all batteries connected with the balance leads in parallel. Example of a 3S JST-XSH balance port parallel harness.  It will be best if the batteries are in a similar discharge state but not an abolute requirement.  Once again, read up on this subject before commensing (RCGROUP thread is a good resource).  I often will run 2 batteries in a plane in series, but then charge in parallel.  One down side is it's much harder to see a degraded pack after/during a parallel charge. It's advisable to individually balance charge them once and a while to see the health of the pack or to keep track of the pack's Internal resistance value if your charger can measure it.

Charging in Series
Although you can do this, I don't recommend it. If you have 2 discharged packs that are not identically discharged, the overall time it takes to charge will be much longer. Especially the balancing phase.  One pack will achieve CV (constant voltage) mode before the other, the charger will reduce current and the 2nd pack will take much longer to finish charging.  2 3S 2200mAh packs for example that might take an hour to charge in parallel could end up taking HOURS to charge in series if you did not discharge them the same.  For this reason most people will parallel charge packs.  

Other useful info
Internal Resistance
One of the most underdiscussed and actually very importan aspect of a battery is Internal Resistance.  All battery cells have an internal resistance that has an important effect on performance.  Following Ohms law (V=IxR), there is a voltage drop in battery output where the voltage drop is proportional to the Current the Battery is putting out (I) and the Resistance internal to the pack (We abbreviate that as IR for a battery's Internal Resistance).  How you see this realized is when you put a load on a battery (battery delivers current) and the more current it delivers, the lower the voltage output of a battery.  Yes, Not only does a battery voltage drop as the battery capacity is used up, but the more current you pull from a battery, the more it drops the voltage.  The lower the IR, the better the pack performs (typically measured in milliohms for LiPos).  Where does that loss in voltage go? Heat is the answer. The pack gets hot.  The higher the IR, the hotter the pack gets. That means at higher current draw, energy is wasted and turned into heat.   Quite often, when a motor bogs under load, it is likely the battery performance than the motor (if the motor was properly sized).  Most of the time, a battery from the same manufacturer will have a lower IR per cell the higher the C rating.  Not all manufacturers are rating their packs the same, so you can't compare a brand X 25C pack to a Brand Y 25C pack and expect the IR to be the same. More often then not, they aren't.  You also can not coorelate C rating to an exact measurement of IR.  Larger capacity packs of the same C rating typically have a lower IR per cell than smaller capacity packs.
One way to quantify the affect of IR on motor performance is with this motor calc tool:
ADAMONE CALC
Simply change the resistance per cell value around and see how the motor RPM and Wattage changes.  
For RC Airplanes, a Lower (Better) IR per cell value will give you MORE peak thrust/RPM. It will slightly increase your flight time as well as the needed Throttle you give the plane will be less because more power is transfered to the motor than given off as heat in the battery.  
For RC Helicopters, the lower IR battery pack will yeild a higher RPM (non-governed) during hover and flight.  Flight time will slightly increase but more if you lower your throttle curve to compensate back to your original RPM when using the weaker pack.  You will also notice the total power in the helicopter increase as you give suddend pitch increases and the "POP" in the helicopter improves (less bogging at full positive or negative collective).  
Many of the newer chargers (Like the iCharger series) measure Internal Resistance per cell.  You can measure the IR and track the IR during the life of the battery. A faulty cell(s) will often be marked by an increase in IR.  Puff a pack due to drawing too much current, overheating it (poor ventilation) or running the pack down too low and you could see an increase in IR for one or more cells. This damage in increase of IR is not recoverable.

Useful Links to read:
RCGROUPS Battery Guide Thread
HeliTown Guide