If I understand this is more of a coding question. I'd argue it would be best for most web based SaaS to have a single codebase, with a single branch that represents the production site. That code base would then be smart enough to enable the right features based on the current user and/or tenant and their subscription level and payment status. Pseudocode:

   public DoFoo(){
      if(CurrentUser.IsFreeSku && CurrentUser.FoosThisMonth >= 10) return Error('Free users are only allowed to do 10 foos each month);
      FooService.DoFoo();
      CurrentUser.FoosThisMonth ++ 
   }

Similar in the UI you may hide or show things based on the current user/tenant and their sub level.

<div class='hidden-paid-user'>Click here to get our paid service</div>

You would still have server code enforce the subscription level rules because a malicious user could circumvent any client-based rules. How exactly you do both will depend on the framework your saas uses.