You can try this a different way. Try creating a basic my-crossover-ms-word.desktop with the command you would run in that AppVM. Then copy that to the template in /usr/share/applications. Force a sync of the menus in that template, and finally go to the AppVM qubes dialog and add your app to your AppVM menu. As long as you know to only run the program in that one VM then you are OK if it's not actually installed in that template.
Once it is in the menu you can always go back and diff the changes and see what edits you should have done manually. I find it's just easier to let the system edit the menus, because otherwise it will just get overwritten sometime anyway. As long as you remember to copy those desktop files to the next template upgrade version, it should just work like any other standard application.