I had the same problem from the first day. I could run a drive in the bottom tray but if I put one in the top tray it would overhead immediatly. The problem IMHO is a combination of things - rear 80mm fans are not in line with the drive bays, the hotswap backplane blocks airflow to the rear, and if you have a power supply that is not vented internally [my seasonic pulls air in from the bottom and exausts out the back with no internal draw] facing the drive bays, there is little or no air movement to the rear of the bays no matter what fans you put in the lower deck 80mm spots. Not to mention that cables coming out of the power supply contribute to the air flow problem, even if you have a mesh back power supply that can draw air. The size of your power supply can also be a factor even when using the supplied "extend to the rear" bracket. I purchased a longer externder for the power supply, which moved it back even further [ 1 and 1/8 inch], this improved the situation however now my power supply has a portion of the intake outside the case, not ideal. I finally realized that this situation was not going to get better, there is IMHO a design flaw here. So I came up with a better answer, and am implimenting it now. I purchased a ICY DOCK SAS/SATA three bay in two 5.25 mobile drive rack, on sale for $23 after rebate, built like a rock with a fan [removeable] on the rear. I put this Enterprise class rack on the LEFT side of the case in line with the 2x 80mm fans. Now, for a couple of bucks more than the power supply extender bracket, I have solved the hot HDD issue, dumped the flimsy, prone to shorting X-dock and it crappy trays, added another drive [three drives vs. two in x-dock], and have an impressive looking and fantastic working mobile drive rack.
Now I have removed the x-dock, and intend to mount a laptop Bluray drive [with four SSD mounting points] in a 5.25 x 1 space and a AFT USB 3 / multi-card reader in the remaining 5.25 space. Niether need the cooling a spinning HDD requires to have any chance of living to the end of warranty. This will require drilling a few holes and cuting the front case metal, and the plastic bezel, but it has been done before and I will start on that part today for my case.
Note I have the HAF-XB non-Evo, so I had to drill out the rivets on my case to remove the cages. I don't think you have that problem. I had consdiered even purchasing the EVO until I found out it had the same exact HDD x-dock overheat issue.