Are you bench bleeding them first? You should mount the MC in a well protected vise, install the appropriate sized block off plugs in the brake line outlets to prevent the flow of brake fluid out. Then route two clear hoses from the bleeders back into the resouvoir itself. Loosen the bleeder screws. Fill the res with brake fluid and using a rod or screw driver, push the rear plunger in slowly and watch the air bubbles. Then slowly release to pull in clean fluid. This could take a few dozen times to get all the bubbles out of the internal passages. Push slowly so as not to foam the fluid. Once you get this done, put the lid on and mount the unit in the car. Then remove the outlet plugs, hook up your brake lines to the MC and bleed the entire brake system starting with the wheel that is farthest from the MC first. This should work if your MC is in proper working order to begin with. I would venture a guess that the Pep boys MC did not have the external bleeders that the original GM MC has, and that is one of the reasons why is is much easier to bleed.
Good luck