You can add custom file extensions to CodeKit's list of languages:
Open Project Settings and select the Other category under Languages. Click the add button in the top table to add a custom file extension.
Next, select an extension. The window shows the same controls that CodeKit offers for every other language. You can set the starting Output Action and Output Path style for files with this extension. For details, see Setting Output Actions & Paths.
You Probably Want a Hook, Too
If you add a custom language to CodeKit, you likely want the app to actually do something when you process files of that type. That's what Hooks are for.