In answer to your questions:
1. Clipper is not a plugin, so is designed specifically as a theme which will run on a WordPress installation. If you wish to use it in conjunction with an existing site you could potentially do so, perhaps by installing in a subdirectory:
e.g.
yourdomain.com <== Your existing site
yourdomain.com/coupons <== Clipper
2. Our themes are not encrypted, so you are free to modify them as you wish.
3. Clipper is a stand alone theme, so plugins are not required in order for it to function. Thanks.