Like the others said, yes, you need to center the box before installing the steering wheel, steering shaft, or spindles. Easiest way is to temporarily connect the steering wheel and count the rotations. with the old type box you should have about 540* rotation. That means you should have 270* either side of center. The new type box I believe has a little more rotation available, but the method is the same. Once you get this right, lock the rack in place, remove the steering shaft, re install it so that your steering wheel is centered, connect your spindle arms, and set toe.
It should be pretty straightforward.