Ideally the fuel/water separator should be drained with some set frequency......maybe every other fill-up. Contaminated fuel is not the only source of water in fuel........condensation occurs as well. If you're pumping 50*F fuel out of an underground tank and it's 85*F outside, some condensation, although slight, is entirely possible.
The key is to drain it with some frequency to prevent the water-in-fuel light from coming on........preventive maintenance. If you wait until the water-in-fuel light is on, it's too late and given the complexity of the CP3 and today's newer fuel injection systems on diesels, draining occasionally is cheap insurance.
The CRD gets drained every 3rd fill-up; my 2003 Dodge RAM 2500 CTD gets it about every other fill-up.
Greg