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.
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.