Yes, I wouldn't recommend running from Dropbox either - if nothing else, you can accidentally delete things too easily. At least if your PAW version is a different copy, you've always got some sort of basic backup.
If you're not already I'd really recommend keeping your code under source control. If you don't mind it being public, you can create a free Github account (you can create private repositories, but you need a paid account for that). Alternatively, if you get a paid PAW account you can host your Git repository here.
While something like Git takes getting used to, if you're planning on creating an app that you're going to maintain, even just for your own use, it's well worth it in the long run. You see this page as one of the many that explain what source control is and why you want it. However, Git is just one suggestion - any source control system is probably fine (except Visual Source Safe, which is just plain broken).