You don't realign the rotor (unless it is bent), you adjust the caliper. For gross misalignment, you will need to loosen the mounting bolts between the caliper and frame and center the caliper over the rotor.

For finer adjustment, the adjustment screws on each side of the caliper should bet you where you need to be. It is most common for a single pad to move when the lever is pulled and the rotor bends to meet the opposite caliper.