As far as I know, Flash (on its own) cannot access drivers other that the ones already given to it. (Keyboard, Mouse, etc.) I've seen other people combine Flash with Java or C# to access the drivers, but none with just Flash. You may need to download a program that converts controller/gamepad inputs to keyboard/mouse inputs, such as Xpadder.
As for the second question, Flash only supports once mouse button for clicking. (the left mouse button) Right clicking is reserved for the little Adobe preferences and "About Adobe" menu that you see in every Flash game, and middle clicking (mouse wheel click) is not supported. However, Flash does recognize the mouse wheel being spun, so you could use that, but it would have the same capabilities of a button press.
I think if you look around, you can find tons of resources on this. I've seen Flash work with controllers for xbox, playstation, wii, as well as kinect and even completely custom-built controllers. You just have to look for the right library or tutorial
