Yes, I'm running Whipples with their innercooler. We've kept the stock raw water pump from Merc (these were 500 efi's), eliminated the circ pump and went to a cross over. The discharge out of the raw water pump tees off to the chiller. There is still plenty to cool the engine, and maintain about 18 lbs. of water pressure from 2800 RPM and up.
My water temp never goes above 120 and stays at 100 unless we're running 4000 RPM or higher for an extended time (which is about where boost kicks in) in which it goes to 120.
I'm runnin Bravo XR drives 1.36 ratio, with low water pickups. Dustin has recommended separate pickups for the chiller and engine where you don't have enough water pressure, but that hasn't been a problem.
This is a triple engine installation in a 43' Black Thunder, app. 13,000 pounds.
Hope that helps you,
Steve