Oh wow, excellent! I think if you just had ye-standard folder selector for the non-sandboxed version and a quick description of how it works under the General preferences menu, that would be fine (for me at least).
I don't know much about the restrictions of sandboxed apps but if for that one you just had Dropzone generate the watch folder and provide a path and/or a reveal in finder option instead, that would be fine. It might be less convenient if someone wanted to have their Desktop or Downloads folder or something there, but probably better than nothing if the app doesn't have access to the rest of the file system (which I'm just assuming is the case).
Looking forward to future versions of Dropzone, I use it every day as a bit of a power user and it's a fantastic utility. If you're ever looking for beta testers I'd be glad to help!