You can download the second beta, or check the main Project Amy account for the most recent version. Once you install it, go to File > Preferences > Accounts, click the plus to create a new account, and select App.net as the service.
The accounts you follow on App.net will appear in a collapsible, searchable section in your buddy list, and Streza says the whole thing is built with the plugin architecture Messages supports. You can even search for recipients when creating new messages (check the gallery), and they will be marked with the App.net service name.
While Apple’s iMessage service may have its issues, Messages is a great app, and now you have a sanctioned way to use Messages for App.net PMs.