To use RootCloak Plus correctly you need to fill a series of requirements. First of all, you obviously need to have a rooted device. Secondly, you need to install Cydia Substrate.
The difference between using RootCloak Plus and deactivating the root is simple: if you deactivate your device's root, none of your apps will have root privileges for that time. If you use RootCloak Plus, on the other hand, the rest of the apps will keep working the same way.
RootCloak Plus is a very interesting app for users of a rooted Android, as it's relatively normal for some apps to not work with this type of device.