you can plug it or run it to the bottom of the header tank and use that point as the fill point for the water system. A lot of cars just fill off the water neck at the front of the head. If you fill through the water pump heater inlet, keep the header tank above the top of the head, and run steam bleeds off the top of the radiators, you won't have any air buildup in the system and it will be easy to bleed.
With a new water pump you might want to compare with your old one - sometimes the impellers are trimmed to reduce cavitation at the higher RPM we run.