Most times just a clamp will push it back in but if it gives too much trouble you may need to loosen the bleeder. Some rear pistons for disk brakes need to be turned back in and a special tool is available for the job at your local parts store.
assuming that nothing else is wrong. when changing the brake pads use a big C-clamp or some vice grips to retract the cylinder. if there are two cylinders you may need to put an old pad between the...