I have a Futaba Skysport 6 Radio and in trying to setup my rudder I noticed it is not exactly zeroed,(mid travel) is there some way besides the trim slider below the stick to zero this servo, either in the Tx or the Servo itself? I have tried repositioning the arm but it still comes out slightly offset. Would like to get it to center with trim in center so I can get equal throws both sides.

The servo output shaft has an odd number of splines so that you can find the center. Try turning the output wheel (arms) and try different spots. One of them will be center when the transmitter stick and trims are centered. Any offset will be at most 1/2 of a spline, which is negligible.