First thing is you need to work out the dimensions of all the pieces - button holes as well as the overall width of the button, joysticks, spinners, trackballs. It depends on what you are going to be using. Next just sketch how you think you would like it to be layed out, joystick on the left (or right?) of the buttons. The number of buttons. Do you want them straight across, on a diagonal, curved. I have two rows of three which is curved to where I feel my fingers are comfortable and another button for my thumb which is near a neogeo layout. Try to have the buttons close together as you don't want to have to stretch your fingers out - would be too uncomfortable. Think about the angles of your wrist and forearms, just like if you are sitting at a keyboard. Do a full scale drawing of it and just see if it is comfortable putting your hands where you imaging the buttons. If it's good then transfer it to cardboard and really see how it feels.
Hopefully this should get you started.
Cheers
-cdbrown