I think that's one of the things that Bettercut doesn't allow you to do. If you want app folders, you can get "Apps Organizer" which allows you to setup custom categorized app folders and freely change the icons.
If something doesn't show up in the edit list, you have to make a new shortcut and find the activity in the (obscenely long) activity list for programs. There should be a launch activity or one that just has the same name as the name of the app, and using that should create a normal shortcut launcher for it.
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