How do I enable an app to work in Messages?

Many apps that you downloaded from the App Store are compatible with the Messages app. For example, if you have Words with Friends, you can play that against a friend within the Messages app. To enable it you have to go to the iMessage App Store by opening any conversation in Messages and tapping the "A" button to the left of the text box. Then tap the four oval icon in the bottom left, then the blue "+" Store button. Now tap the "Manage" tab and you will see all of your apps that are compatible with Messages. Toggle on the ones you want to use. See here for more information on installing and using apps in Messages.