What the best way to build two versions of a game?

I decided to make my single game into two different versions:

  1. free with Unity Ads
  2. 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?

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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…

http://unityads.unity3d.com/help/monetization/integration-guide-unity

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Thanks, I actually read through all the docs couple of weeks ago without noticing that!