Hmm. This is the first time the flow of the game is disrupted for me. I've shot the yellow box and extended the bridge over the electrified water, and it the switch that raises the floor in the big room. In the big room, I can only get to one of the "goodies" shelves, the center one. Besides that, there doesn't seem to be anything to do...
You know the room you have to shoot the yellow box from? The other bridge in the room on the bottom level should have extended, opening the door in the center column.
You cannot proceed through the training room, go back to the small control booth that had the crate you shot in it. There is a control panel there that lets you get into the center machine in the middle of that blue liquid.