Well, you obviously know what the controller looks like and how it functions. What you may not know is how the buttons from the controller are laid out across the stick. If you do, forget the this part and go to the next, if not read this. I use a 360 controller, so the top four buttons are X Y RB LB, and the bottom row being A B RT LT. Going from the regular controller to the TE stick they change button locations. Because of the change in button locations, people change their button layout in the SF4 or MvC3 menu.
Depending on what game you use, people have different preferences. Some people also prefer the first “slant six” button style, and some prefer the “inline six” buttons and remap accordingly.
I use the slant six buttons, and for SF4, I use X Y RB as Light Medium Heavy punches, and for A B RT same order for kicks. On MvC 3, I use X Y RB as Light Medium Heavy, and A B RT as Special, Assist 1 and Assist 2.
Hope that helps.