We have done it with our middle school several times. It is awesome. The tour we have done has been you show up a little before closing, put your stuff down, meet your guides. There is a little bit of animal tour, some behind the scenes stuff (like walking above the shark tank) and dinner. Then some more animal tour, education stuff / games / information and then you set up for bed. We got to watch a dolphin training session just us because the aquarium was closed to the public at that post. And kids could ask 1 million questions. Wake up the next morning, a little more talking / information, breakfast and then you have to leave (we put our stuff on the bus) but you get a stamp to the enter the museum and see the stuff you did not see before.
Kids always have a great time. You do sleep ON the floor, so that is uncomfortable at 37, but 12 year olds don’t seem to mind.