You multiply the C rating times the battery's capacity. This tells you how much energy the battery can safely 'dump'. A high C battery can dump a lot of energy at once, whereas a smaller C battery is for less demanding applications.

Example: 1000mah 50C battery: 1000mah x 50C c= 50,000ma, or 50A.
Example: 1000mah 25C battery: 1000mah x 25C = 25,000ma, or 25A

When you look at your system as a whole (motor, ESC, battery, prop) and determine how much current you expect to pull, you can decide on a C rating. If you are only going to run at 20A, you don't need the 50C battery.

Higher C batteries weigh more (and are more expensive). There is no need to get more C than you need, unless you just want that extra little bit of power.