Assuming those are control signal inputs you are talking about they would be connected to Servo outputs on the Flight controller. You have assigned throttle and steering outputs right?
Most modern flight controllers cannot read each channel of the RC input separately. If you can, configure your receiver to send one of the protocols listed here: Radio Control Systems — Rover documentation
If that is not an option, you can get an external board that will combine the signals for you, such as this one (I just got the link from a keyword search, have not bought these in a while)
I think those boats come with a receiver that is meant to connect to individual servos and ESCs (speed controllers) like an ordinary radio controlled model.
You either need one of those adapters to combine all the PWM signals into one PPM signal for the flight controller - or get a new receiver that has a single output for PPM or SBUS, something modern.
The servos and speed controllers plug into the flight controllers servo or “main out” connections.
Sure. Connect the Receiver outputs to the Motor ESC and Steering Servo inputs and drive it manually. Most RC vehicles are setup this way. People add Flight Controllers to Rovers and Boats to do some assisted or automated things.
In fact driving in manual Mode is essentially bypassing the Flight Controller although there are some useful functions.
If you don’t have a need for a controller then don’t use one. It’s as simple as connecting the Rx outputs to the Motor ESC and Steering servo inputs. What RC system do you have?
Not much point in that if you are just going to drive the boat manually with a 2 channel RC system. Isn’t that pretty much off-the-shelf from Horizon with that boat?
I think Dakota is talking about an RC “Controller” (transmitter and receiver) and Dave is talking about a Flight “Controller” (autopilot).
If you want to use the autopilot for assistance and automatic features, you still need the RC transmitter and receiver in order to do tuning and set everything up properly, and to take over in case something goes wrong.
Then you need a Flight Controller. You need an RC System also to get the boat configured and tuned properly. After that you could control it from a ground station but you need it initially. And the RC system it came with (if it came with one) is likely too limited to suit.