You let air into your lines...you'll have to bleed the brakes until you get everything out. Youre NOT supposed to let the brake resevoir get to dangerously low levels while bleeding the brakes.
Go to home depot and buy some clear plastic tubing (I believe 3/16" will work) you'll only need about 2 feet of that stuff, take the tubing and put one end over the bleeder nipple and the other into a jar with about an inch or so of clean brake fluid. p.s. if you tape a lug nut to the end of the tube that goes into the jar itll help keep the tube submersed in the clean fluid...that way you wont accidently let any air back in.
Procedure for bleeding the brakes would be to open the resevoir and fill it up to the max, have your wife pump the brakes 3 times and hold it down on the 3rd pump, then you open the bleeder nipple 1/4-1/2 turn for 1 sec then close it, make sure she keeps the brake pedal depressed to the floor until you close the nipple, once its closed have her pull the pedal back up and pump the brakes 3 more times, open the nipple again...repeat that until theres absolutely no more air bubbles coming out of the clear plastic tube. Hope this helps you.