Well, just like every offense I've ever heard of, all the offensive coaches get together and make up a game plan with the calls they intend to use for the specific opponent during the week; and then somebody surveys from the press box and calls the plays down... no different with Cut and Roper, and Roper has been that guy since 2002.
A quote from Cut during an interview while at Ole Miss...
Head Coach David Cutcliffe Holds Preseason Press Conference
Rebel leader talks about upcoming season with media members.
Q: Much was talked about how effective Eli was at changing plays at the line of scrimmage. How much will the offensive play calling change with a new quarterback?
A: We won't change our philosophy. Our offensive philosophy is to try and train the quarterback to put us in the best possible play he can put us in. Micheal has been in the same system Eli was. When you are a first-year starter you are not quite as comfortable with all the different realms that Eli was given, but we'll be similar. We try to teach them everything we know and they're the functional part. If they know everything they're supposed to know, they should know more than the coach. That's the challenge with a new quarterback.
Q: Who's all involved in that process?
A: Kurt Roper has the responsibility of calling the play itself. The entire offensive staff develops game plans. Kurt starts the process from the pressbox by signaling the play down to the field. Then coach Woods and the quarterback have options based on what is signaled.
Head Coach David Cutcliffe Holds Preseason Press Conference - OLEMISSSPORTS.COM - OLE MISS Official Athletic Site