You can deploy multiple web applications as part of the same Apprenda application by including the different web applications as different folders inside the interfaces folder. One of them should be called root which will be the root of the website and the other should be called whatever name you want it accessible as for example:
You may have two web applications, one for the main app and the other one for administrative purposes. You should include both of these web applications inside of your interfaces folder as root and as admin. When deployed by Apprenda you will be able to reach them at http://appalias.cloud-url/ and http://appalias.cloud-url/admin/
Hope this helps.