I changed the brake pads on my rear brake a few days ago.  I did take the caliper off the disk, but left it connected as not to lose the fluid.  I pushed the pistons back in (lost a little bit of fluid) and put everything back together.  Everything fit well and I topped of the brake fluid.  I do plan on changing it in a few days. 

Since changing the pads I have much less braking power out of the rear brake.  I have to push down further before it begins to engage as well.  Any ideas what could be wrong?

Did you put in different type of pads? There are different pads with different performance ratings. Which rating were the pads you put on? FF, GG, or HH?

Otherwise, it takes brakes about 100 miles of city stop-and-go traffic before they become the most effective. Give them time to mold to your rotors. They'll have reduced stopping power until then.

I put in the EBC organic pads.

Those are fine. Still have to break them in, though