I'm a JR user myself but i do setup allot of Futaba equipment and IIRC the flaps come assigned to the left slider and you just go into the AUX Channel and assign that channel to whatever switch you want the flaps on, they'll then be 0/50/100 with the 3 position switch. you can't adjust the 50 so set it mechanically to what you want then use end points to set full up and down flap.

and you may not belive this but AFR means 'primary rate'