I decided to make my single game into two different versions:
free with Unity Ads
not free, but no Ads
What is the best way to do so?
Should I start a duplicate unity project for the Ads version? Or should I just build the same project twice with different settings & scripts?
Definitely a single project. Maintaining multiple copies of any application, especially when they have differences, is usually a very painful experience. The Unity Ads intro even covers this, probably time to go read the docs…