Thanks Steve! Not only is the 5 1/4" drive bay mod for aesthetics but I needed to cut the top portion out for the 420 rad to have airflow on the front most fan.
There are 4 ports on the apogee but to be honest I can't answer your question. My guess is just for options on fitting placement. I just bought it because it looks cool and it has one of the easier mounting systems(my raystorm was a pita to mount). It also did very well in the 2012 CPU block roundup found on another site.
Also here is what will be going in there. It will be a black and yellow theme. I chose these colors because these fans have great static pressure and you rarely see a yellow theme build.
Also MDPC Shade 19 and Yellow for the sleeving. I will be re doing all of the wires to custom length.
I will also be painting the tips of these bad boys to imitate a dominator look. I got the last ones in stock. :D