I purchased the wpbakery license at Themeforest.

Should I remove the version that came with the PenNew theme and install the version that was made available for download?

I contacted Wpbakery support and this information was passed on:

You need to contact the theme developer and check with them if the theme is hardcoded using WPBakery or if you can install a standalone license on your end. Some hardcoded themes can crash if you install a standalone plugin, that is why we ask the customers to contact the theme developer to be sure.
We are a family owned and operated business.
If you need further assistance, please let me know.