RE: Futaba 12z
AFR is where you set dual rates, or otherwise reduce the throw of a given control from the maximum that was set in the ATV menu (under linkage). You also set expo in the AFR menu.
If you are suing conditions (and you should be) you can have separate throws on everything by having a unique AFR value in each condition.
So what you do is set the maximum control travel in the LINAGE->ATV menu. Then you reduce that throw as you want using the MODEL->AFR menu.
ATV applies to everything, hence it is in the LINKAGE menu. AFR applies to each condition for that mode, hence it is in the MODEL menu.