Users who activated Coin Control (see How to use Coin Control) probably noticed a extra part underneath the "Inputs"-button:
The advantage of using this option is that all "Change" coins, when performing outgoing transactions, will be stored on the same "change" address (the one you put in the input field, after checking the checkbox). This way your wallet will not have several change-addresses with different amount of coins on it, like this :
The address on top (marked with n° 1) is the main address.
The address in the bottom (marked with n°2) is the change address. This is where the remaining coins were stored after the outgoing transaction.
To avoid having your coins split over several addresses you can put the main address in the "custom change address" field.