i had this problem with S197 mustangs when working on them without a battery installed.
i had to connect the ground wire to the ground. the thick positive wire to the positive on jump box. and the thin wire that signals the window to roll down slightly when opening the door to positive also. the windows will roll down this way.
their are signal wires for both the L & R side doors. their are also signal wires to roll the window back up also. their is also a wire for memory on express up and down you don't have to worry about.
i would ASSuME the wiring is the same on a challenger.