Maidhc O Casain
Na Bith Mo Riocht Tá!
When I run one, I treat the Gestalt classes as a new, single class. Characters are welcome to multiclass, but their multi-class option will not be a Gestalt one. So far no one's taken me up on it . . . 
I also allow only one of the classes to be a caster of any kind.
So if you want to play a Gestalt Ranger//Wizard, you'd have to take a spell-less Ranger archetype such as the Skirmisher. If you wanted to pick up a level of Bard or Rogue later you could, but they would not be Gestalt levels - it would be Bard or Rogue only.

I also allow only one of the classes to be a caster of any kind.
So if you want to play a Gestalt Ranger//Wizard, you'd have to take a spell-less Ranger archetype such as the Skirmisher. If you wanted to pick up a level of Bard or Rogue later you could, but they would not be Gestalt levels - it would be Bard or Rogue only.