Rogators that used a Servo Valve for product control often utilized three wires.  The connector that was used was a 4 pole AMP connector of which 3 pins are used.  Two of the wires are the Inc/Dec pair that actually turn the motor on top of the hydraulic block to adjust the oil flow which eventually determines the pump speed.  This pair connects to Pins 3 & 4 in the 16 Pin Connector that attaches to the Raven console.

The third wire was a "Valve Max" indicator.  This wire leads to a black plastic box with an LED in it on the steering column. The idea was that this gave the operator a visual indicator that the valve was opened to its maximum and that reducing ground speed will probably be necessary.

Rogators that use the PWM concept for product control often require the use of a Raven 661.  This console is like a 460 but has a heavy duty PWM circuit available in the 14 Pin connector.

With the information you have presented I would guess that your rig is using a Servo Valve.  I believe you will need to bypass the armrest section control wiring.  You would then use the switches on the Field IQ switchbox.  The wiring from Field IQ would lead to the various section valves.  Since you are adding sections, this would be a good time to "clean up" the wiring to those areas.