Say, if you have a piece of 10btc, and want to send 5btc to Amy.
The tx you created would be:
(1) Input = that 10btc
(2) Output 1 = 5btc to Amy
(3) Output 2 = 5btc to your change address
No worries, you wallet would calculate your balance correctly.
Different wallets have different ways to show the change addresses.
For example, if you are using bitcoin-qt, you will not be able to "see" your change address in your receive tab.