From looking through the documentation at developer.boxee.tv I have found that there is a much easier way of adding your apps to Boxee for testing. You simply need to add the following into the app element in your descriptor.xml file for the app:
When you start Boxee it will look for any apps in the UserData/apps directory with the test-app property set to true and automatically add them to your apps. Once you have finished testing your app, simply remove the test-app element or change it to
<name>My Test App</name>
<email>my email address</email>
Doing this will remove it from your apps when you restart Boxee and you can submit it to Boxee or add it to your repository.