The setup with the plug installed can be confusing. You may have to do a couple of times to see that you move the sticks the proper way each time.
When you get done the surfaces in normal mode. If my memory is correct is orange with the gain turned way. Will move the direction you move the wing, Wing up and aleron moves up. lift the tail and elevator moves up or you can raise the nose and the elevator will move to correct.

The rudders will correct the nose heading.

It should matter if you have 2 rudders or one because in the setup the Cortex reads the input signal each time you move the sticks for the correct settings

Here are the instruction that I am speaking of. If you notice you move the stick after every single twitch. I got the rudder wrong a couple of times before I got it right.

• •
(switching on) → Leave the sticks neutral, wait for signal
• •
(2x)
→ Now hold aileron at right-hand stop
• (1x)
→ Now hold aileron at left-hand stop
• • (2x)
Release aileron
→ Now „ress“ elevator on stop and hold
• (1x)
→ Now „ull“ elevator on stop and hold
• • (2x)
Release elevator
→ Now hold rudder on right-hand stop
• (1x)
→ Now hold rudder on left-hand stop
• • •
(Servos 3x) •••••••• (LED flashes green

Pull the setup plug and check directions
.