I had the same problem. Only with an older HDD, but the only two ways I found to get around the issue was to put the drive in a 5 1/4 bay (with the appropriate adapter) or cut away some of the metal in the HDD bay infront of the hard disk.
Each has its own limitations. If you cut away part of the metal, make sure it is straight afterwards to aviod HDD noise. This is what I did, and afterwards would have prefered to use the other option. (This option will likely only work if you use RAID as JOBD, as an IDE cable will not reach from the HDD "tray" to the top 5 1/4 slot (to link to the DVD drive if your is IDE). If you drop your DVD down it might fit, but mine would not.
Note the above assumes an IDE DVD drive that is a slave to the IDE HDD.
The simlpest way is to put the IDE drive just below the DVD drive. No real HDD cooling here.
Anyway, there may be others but this is what I found.