You need to remove the cap, top off the fluid, crank it up and turn the wheel lock to lock a time or two, then recheck the fluid. Repeat the procedure until it stays topped up.
As far as what you already did, you almost did a proper flush. The correct procedure is to remove the return line, place it in a drain pan, start the car and pour two quarts through it while an assistant turns the steering wheel back and forth. Then hook up the return line and follow the procedure in the first paragraph.
Don't worry, I'm sure that once you bleed it as I described, it will be okay. Don't use ATF, use power steering fluid from the auto parts store. Modern Mercon ATF will ruin the seals in your unit. If you insist on using ATF, find some type A somewhere.