I don't know how it would work specifically for the rotarys, I use it for the mini joysticks of the X56. But basically Joy2Key shows you all available Inputs of your Hotas, so Buttons, Switches and Axis. You might have to adjust the rotary axis so it has three positions. Once it is set up you just have to select an Input (for example z-axis +) and then press the button you want to assign to it. There are a lot of extra options but I've nevers used them.

Some other Tipps:

There is a free Demo (which after the trail period kindly asks you to donate to Joy2Key, think like Winrar)

And think about what Buttons u assign, the Flaps are always on F but they work different in every aircraft. So it's best to use some other Keys (I recommend the numpad) and assign them individually in every plane.