I noticed the same thing on mine. New calipers and pads, old rotors. Since I don't have the master cylinder hooked up or any fluid in the lines I just assumed they would set right once I put pressure in the system.

The springs behind the caliper pistons should push the pads out to the rotor. If they don't, it could be due to:
The springs are weak/broken
Pistons are hanging/dragging in the caliper bores
The rotor may not be exactly centered to start with.

The calipers are "fixed" in position...meaning they do not move. If the rotors are not sitting in the center of the caliper opening, they may not be right for the car, depending on how far off they are. A little bit is ok, but too far off would make it hard to get the pads back in on one side.

Adams I have pads on the caliper and on to the rotor. When I look at the top of the caliper you see a little more piston on one side then the other. I thought It had to be perfect center. I put a shim on one of the brake pads it made it a little better.

As long as the pistons are still in the caliper housing when the pads are worn down, you should be fine. They do not need to be perfectly centered. You may notice more wear on one pad than the other anyway.