OK Masonz I hope this helps you out...
This is where I moved the large fan to that originally was the top exhaust fan, all I did was remove the 4 screws and placed it here.

The one on the left is the fan for the video cards, and as you can see the two on the left are the ones for the hard drives.
Fan control sliders on top of case, room to add more as needed. This is my setup.

Also If you are worried about the getting more air into your case there is an optional spot for another fan in the front.

Also both of the side fans on the HD's bay are controlled by one wire, I have had no problem with the connection.

And if you are worried about airflow over the hard drives this picture you can see that there is a complete aiflow through the case.

I hope that haelps you out
LawnDart