When I do front Brakes ( have gone thru 4 Caliper units and on 3rd set of rotors) I Always remove the banjo Brake Hose and replace the Copper washer and also the Stainless pad sliders. You can push in the piston easily.
I don't understand what you mean by one side goes out when I do the other? I hope you are doing one side at a time, if so put back one caliper with the old shoes so they just fit back over the rotor on the one side.
2 ways, first take the c-clamp from behind the caliper so the screw with end joint is on the back of it, place small piece of wood or the inside ***** out pad onto the piston (edit: evenly over the two) and tighten it until the piston(s) is seated home. Complete that side of the truck, move over to the other side and repeat. if the brakes are worn out the piston fully extended will feel like it is stuck but with the clamp centered behind in the middle of the piston it should go easy.
Otherwise disconnect the brake hose and replace the copper washer (Once new pads are on), bleed the brakes.
I have found with this method that the Torque spec for that banjo bolt is not enough because it always leaks afterwards so I found that an extra 1/4 turn usually is enough to remedy the leak.
I always torque the small long bolts and or caliper mounting bolts to spec and use blue thread locker on the bigger ones. Got the specs here somewhere if you need them.
Good Luck, and try not to be frustrated. Danny