In general, system installation with the Ninja case is very straightforward, with only a few things to watch out for.
Firstly, popping the black covers out of the front panel which cover the drive bays is surprisingly difficult and required a fair amount of force. Be careful not to lose skin doing this.
Secondly, as already noted, the hard drive configuration does draw the drive connections further away from the motherboard. This probably won't be a problem for the power leads which are generally long enough to cope, but depending on the positioning of the PATA/SATA ports on your motherboard, the data cables could be a problem. Especially with a master/slave PATA configuration - in this instance it's probably worth investing in pre-cut ribbon cable which tends to be much more flexible, or you can cut the cable yourself and bind it together.
Finally, full-length optical drives mounted in bays 2, 3, 4 or 5 may come into contact with diodes or capacitors mounted on the extreme left hand edge of the motherboard - something to watch out for.