It depends on what you'd be Water Cooling. If you were Water Cooling your CPU you'd see lower temps than on a Tuniq Tower; significantly lower temps. If you got a nice $250 Swiftech Apex Ultra Setup and got a VGA Water Block you would see a very nice drop in temperature; however, for a 6600 I would not recommend Water Cooling. For your rig I'd get a nice 7-Series nVidia GPU instead of upgrading your cooling.
In essence, distilled water and coolant are pumped through a pump, then they travel to your blocks - Processor, Graphics Card(s), Graphics Card Ram, Northbridge, Physical Ram, and/or Hard Drive(s) - then the warm water flows through a Radiator - 80mm, 120mm, 240mm, 360mm, or 480mm - finally the water is taken to the Reservior. Then, the process is repeated.
So, you are asking "How do I use Water Cooling if only my CPU is included in the loop?" Well, the best way would be to leave all of your case fans and your coolers on and just replace the CPU Heatsink Fan with the CPU Water Block. This way, the other components in your Rig are not harmed or touched.
A word of warning; if you are going to get Water Cooling do not get a 80mm radiator and a $20 pump. If you are going to go with Water Cooling it's going to need more expensive than Air Cooling. The minimum I'd spend on Water Cooling would you about $150. You want to get a nice $50 Water Block, $50 Pump, $50 Radiator, $20 Reservior, and Fans. Swiftech and Danger Den are two top brands in Water Cooling.