Ah, in my experience building a computer, not all of the connectors will go to something, and not all of the sockets will have a connector in them. If you have things that won't fit together, they aren't meant to go together. You already know that, of course.
As long as everything that fits together is connected, though, I think you will be good to go. The motherboards and power supplies are designed to make it pretty hard to mess things up.
I may be wrong, though, so I would wait until another member posts here as well.
"Sorry, you can redo your sig...Stupid Mod pressed the wrong button." - JLMoonDog