Based on my 2010 trip in Dubai :
- The best way to travel through Dubai is either the monorail (to go from Mall of the Emirates to Dubai Mall or to the airport) or the taxi, which is really cheap (approx 10€ for a 30 minutes drive)
- In order to get to Aquaventure, you can either use the taxi or the monorail. The monorail offers a very nice view on the Palm and the Atlantis resort but its departing station is in the middle of nowhere. It's easy to get there with a cab but I wouldn't recommand you to use it on the way back : we spent 30 minutes to find a taxi there. If you come back from Atlantis with a taxi, don't wait the park closing otherwise the line will be extremly long !
- As for the sightseeing, I recommand you Dubai Mall (which as Noxegon said features Dubai's best coaster in Sega Republic) and Burj Khalifa. I think the firsty fountain show starts at 5pm and then it's every 30 minutes. A nice spot to enjoy it is the terrasse of the TGI Friday in Dubai Mall.
You can also have a breakfast at Burj Dubai but you have to book it in advance (just ask at your hotel desk, they will arrange it for you). It is the only way to visit this incredible 7* hotel and, well, the breakfast is not bad at all . Other interesting sites are old Dubai with the souk and the Jumeirah Mosquee.
- Last thing : for the luggage, just leave them in your hotel and come pick them up just before you go to the aiport.