And why you have purchased a additional license for WPBakery?
If the WPBakery is included with theme, you don’t need to activate it - all will work fine. But, if there is a new version of WPBakery you can’t update it - you will need to wait for theme author to update the plugin inside the theme and to download a new version of theme and on that way to get a new version.
Of course, you can buy additional license (you have already did) and to get the easy updates without waiting for theme author to update the theme and plugin inside it. But, what if your theme is not compatible with new version of WPBakery? In this case you still need to wait for update from theme author.