I built an exact replica of the C02 Controller. I have the dimensions and all exactly as they are. The only difference from the stock layout I changed was moving the Tornado Spinner. I drilled my hole for the spinner shaft down and to the right of the 4-Way Joystick. It's just off-set from the single button below the 4-way. There is space in that area although it may crowd your 4-way a bit. If you had other areas in mind, let me know and I can look at my control panel.
Question: So you already have your C02 or are you ordering the stick separately?? If you are adding the stick, just see where it fits when you get it in. If you are having it placed on the Control Panel by SlikStik, I would just accept their default layout. Just my 2-cents...