You want the IC pump at a low point, and a way to bleed the system of air.
This would be your basic setup:
HEAT EXCHANGER BOTTOM TO> PUMP INLET
PUMP OUTLET TO> INTERCOOLER CORE INLET
INTERCOOLER CORE OUTLET TO> HEAT EXCHANGER TOP
A 5-7psi cap on the highest point in the lines would suffice to bleed the air out and add more water to the system.