We had a situation where the batter/runner hit a ball off the fence in center field and the ball became lodged between the fence and an advertising placard. A ground rule double was the call on the field. The batter/runner went to first base and left the field because a courtesy runner was being sent to second base to assume the ground rule double ruling. The courtesy runner touched second base. The defensive team claimed that the batter/runner needed to get to second base by himself and that the courtesy runner should be called out. Is this an out ? If so, who is out, the batter runner or the courtesy runner? Thank you

Randall, was this in a sanctioned SSUSA tournament or a house league? Reason I ask is because in a house league it might be ok to do that. I could have missed it but I didn't notice a rule in the ssusa rule book pertaining to that situation, so it's not a question that has a definite answer that I can tell.
It' is best if all runners touch the next base or in your case touch first and second to avoid any confusion on a dead ball situation where bases are awarded.

You have to touch the bases. If the defense "appealed properly" then we have an out. Proper appeals are by the manager and before the next pitch.

Linknblue.. actually the appeal can be made by any defensive player