New Radiator, quick question.

You don't have to do anything to the A/T cooler lines. You may want to cap them just in case later you decide to go to an auto, or you sell the radiator to someone who runs an auto, that way you won't have any contaminants in the line and you can just uncap them and use them if you decide to. But, no, you don't need to do anything special to them since it's a closed-loop system, separate and distinct from the radiator tank.

Agreed. Toss some plugs into the heat exchanger female fittings and call it good.