Do you add the registry keys in the Application or in the installer? If you add the registry keys to the installation MSI they will automatically be removed on uninstall.
To look at information regarding the modifying a distribution kit please see the attachment.
I am adding registry in my application (allow user to select one of two registries). This is implemented in separate application which I execute during installation via Advanced Distribution Kit Options.
What version of CVI are you using? Things are different in differnt versions.
In most cases you would do the opposite on uninstall. You test to make sure you are in uninstall mode and author a way to remove either of the registry keys you authored.