I just got my entire brake system redone (front/ rear pads/rotors) at Pepboys and when I went to apply the E-brake, the car starting rolling down hill. I can put the car in gear still to prevent the car from rolling but what can cause the e-brake to fail?

 

There mechanism and stuff is all behind the rotor on the rears, and is adjusted through a small hole on the rotors. Pep-boys may have knocked it out of adjustment when changing it. Check the 3G garage on how to readjust it.

 

Happened to me as well... local mechanic did not fix the e-brake pad-things.
I ended up hitting a concrete pillar.

csmeance is correct...
Essentially you just need tools to remove the rear wheels [and rotors if you want--but that's just more work].
From there you'd need a flat-head screwdriver to access the gear in the hole that tightens the pads.

 

Thats the correct adjustment procedure, but why not take it back to "the three best friends your car ever had" and let them correct it like they should have the first time.