I have a hydraulic roller and the plunger in the lifter goes down when lifting the valve even with a test spring on it.

What is the proper way to make sure I don't have a valve hitting a piston.

First pump up the lifter with oil or bottom the plunger out in the lifter if you don't have a solid roller lifter. Take medeling clay , place a small amount on the piston so the valves will contact. replace cyl head ,set up valvetrain on#1 cylinder with zero lash, turn engine over til on comp. stroke on#1,remove head check the indent in the clay. Now with a dial mic. place the end of the mic opposite from meas. face basically where the rod comes out . wich is like a hieght mic. Lightly set the mic squarely on the indent, insert the rod thru the clay until it contacts the piston . Thats your clearance!! Now add the compressed head gasket thickness ;usually .039".
I shoot for min. .100" ,,,, hope that helps

you need a solid lifter so you have no compression in the lifter while checking the clearance.

I did pump up the lifter with oil
I never thought about pushing the plunger to the bottom then setting the lash. I did not want to ruin a brand new lifter

nothing in there to hurt

Thanks. It worked just fine