Mercury/Mercruiser? I have a twin engine boat, Mercruiser 6.2L / 350 HP with the Axius joystick system.
Nothing about the transom - not sure what you are referring to.
If your boat is OB's, then it is 3 engines (right) I/O are still 2 (right?)
Anyway, the joystick takes a while to get used to. It is pretty complicated, because it separately manages the steering, gear shift, and throttles of each engine in order to perform the desired maneuvers.
The joystick control works OK . . . I find that the boat goes backwards more than it should, but you can compensate by moving the joystick in a more forward direction. Also with multiple engines you can do many of the maneuvers by just manually controlling each engine.
The one maneuver that I like is 'crabbing' sideways, as it is helpful to move in and out of tight docking spaces. My boat is 7 years old and the system has been working fine. If your boat has battery/voltage issues, it can be a bit chaotic, since all of the throttle, steering, and shifting is electrical and not mechanical. Low voltage can give all sorts problems, warnings, etc. A friend of mine with the same boat, but Volvo engines, had a voltage issue and his steering went into a guardian mode.
Any specific questions, feel free to ask.