Okay, since this is next to impossible to figure out without help - I could figure out the first sequence on my own, but not the second sequence - you're getting a freebie on this one.
First click on the controls to Prescott's left. TAKE THE WRENCH; you'll need it. The buttons will move the crates for you. To get to the glowing box, punch the buttons in this order from bottom to top: 4,2,5,6.
Once you've gotten all three items in the box, go back to the controls and pull the lever to reset the crates to their old positions. Now press the buttons in this order: 3,2,1,2,4,2,5. This will clear a path to the stairs and the toolbox. Get the crowbar out of the toolbox, go up to the warehouse door, and use the crowbar to open it. You'll be able to use the crowbar on the sewer grate, but you can't get down there quite yet...