you need to assign the controller a profile/control scheme from the settings.
If you go to Configure -> Controls -> Controllers (last tab, screen where you can re-bind keyboard etc) you should see your joystick in that list. Click it and at the bottom give it a scheme (default key-bindings based on popular joystick models).
I'm at work atm so I'm probably not being very helpful. But hopefully you can figure it out. If not I'll walk you through it when I'm home.
Then you just need to re-bind any specific features, as you would a keyboard except use the joystick.
If you have a HOTAS I believe you need to set the throttle Increase/Decrease to the Analogue binding instead. Otherwise it might only use the lower half of the throttle.