There are basically 2 settings that are very important when charging your Lipo's.
Voltage or V - You want this to match the voltage of the pack. If it's a 2S pack the charger should be set at 2S or 7.4V, for 3S it should be set at 3S or 11.1V, 4S it should be set at 4S or 14.8V, etc...
Amps or A - This is your charge current and this is determined by the mAh and CHARGE C rating (disregard the discharge C rating 20C, 30C, 40C, etc.. of your pack it doesn't factor into charging) of your pack.
To charge a 2S 5000mAh pack at 1C you should set your charger at 2S or 7.4V and then the charge current should be set to 5A (Amps).
To charge a 3S 2000mAh pack at 1C you should set your charger at 3S or 11.1V and then the charge current should be set at 2A (Amps).
Some batteries can be charged at a higher C rating. For example I have 2 Turnigy packs that don't recommend charging higher than 2C, but my Gens Ace packs are good for up to 5C charging.
I was new to Lipo's a few months ago so I know it's confusing, but those are the 2 things you need to worry about. If say you try to charge a 2S pack at 11.1V that's when you run into problems.
I have a Thunder AC680 and when I go to charge a pack it auto detects the number of cells (2S, 3S, 4S, etc...) I then have to click OK to verify that it's correct and then I select the charge current (Amps) and click OK and then it starts charging.
As a far as balancing goes I'm not an expert, but I balance charge my packs every time I charge them.
Hope this helps.