The version of Final Draft that's in the App Store has the exact same functionality as the retail version you already have. If you're running FD with no problems, there's nothing in the App Store version you're missing.
When we release updates to FD, they'll be available for free from the App Store AND our website.
The App Store version is a separate product from the retail version and owning one doesn't affect acquiring or owning the other. There are no discounts or swaps offered for one if you own the other.