I was attempting to change out my rear brake pads on my 99 civic si and what i did was
take everything apart and took out the old worn out pads and when it was time to reassemble everything i started by clamping the brake line, then loosened the bleeder valve and drain my fluids so that there would not be so much pressure to push the piston back to fit the thicker new pads. this did not help and the piston was still not budging so i took the clamp off the hose and tried to drain all of the brake fluid and i had a friend step on the brakes to push out any fluid but instead of coming out of the bleeder
line it forced the piston to come all the way out and tearing the rubber boot along with it,
what should i do to fix this problem.

 

I think you need to "Screw" the piston back into the caliper.
you should never have to clamp the hose and open the bleeder.