Raymarine autopilot electro hydraulic pump

[Joh. Dijkstra]

I am since 1 year in the possession of a 12 meters long motor yacht, type Grouwstervlet (see www.grouwstervlet.nl) with an open cockpit.
The ship was equipped with a Raymarine auto pilot, type ST6001 Smart pilot (Software version 14 ver. 302 with 270 running hours) with a dashboard control device and 2 remote control devices (ST100 wireless and ST600R wired). I am using the system quite offend also in inner water but notice that passing a steel construction the system will deviate from its course and making a sharp bend. Further more if I want to pass underneath a bridge, I have to lower the mast, in which the compass is installed, and the system deviate also from its course. Having above described experiences, I start to think about a modification and that brings me to the following question.
Is it possible to control the electric hydraulic pump manually, in parallel with the control of the autopilot, by a manual electronic switch or joy stick controlling the pomp to run in both directions. I wonder if it may damage the Raymarine equipment.
The idea is to have the switch available in the open cockpit at the stern of the ship (where a have a motor control as well) either handheld or fixed allowing me to steer from that open air position.
Thanks and with best regards,
Joh. Dijkstra