Shoot, just re-read your post. You're right.

If you're NOT using an EBC, you can leave those holes open.

 

^^Thanks for the detailed explanantion One-Nut, everything you explained is exactly as I had thought, so that's good.

I do have a boost controller, but it is the turboxs manual one. When I hook that up I know I will have to use one of the top air holes and plug up the other one.

This is the rough diagram I was going to go by when hooking it up...
http://www.gnttype.org/techarea/images/wstgate.gif