You can have multiple aliases on you Google Apps account. All email received on these aliases will be delivered to you inbox. When you reply to one of these messages, your primary email address will be used. You can easily change this setting so that you can reply to each message using the address the email was received on.
1. Click on the Gear icon at the top right of your Gmail session.
2. Click on Settings.
3. Go to the Accounts tab.
4. Choose your preferred option under When replying to a message:.