You should not have to remove the rear wheel except to improve access. I usually take the rear caliper off and wire it out of the way before I remove the back wheel. The caliper is held on by two bolts and the rear reservoir is accessable if you take the seat off.
One reason your brakes could go so quick is if the caliper is frozen and you're only pushing on one pad. Check to see that the caliper floats freely.
It is probably a good idea to put new front pads on if you are doing the rear
