In the in-game options, go to the Ship tab, then you may have to scroll down to "Bank Axis" and the other Axis binds. On my Logitech 3d Pro, I think by default when you start a new pilot, it has the Bank Axis mapped to the little throttle control on the stick. So if you have the throttle all the way up, it will make you spin in one direction. All the way down, and you start the mission spinning the other way.
In the in-game options, just bind the Bank Axis to you twisting the stick (Click it, click Bind, then twist the stick and it will say Z Axis), and bind the Absolute Throttle Axis to the little throttle slider if you want to use that, too.
Control settings are saved per pilot.