ReefWaters: Thanks but you'd be much better to ask photography questions from the experts in the photography forum. I am the first to admit that my knowledge is limited at best.

But... what I typically do is to shoot in the AV mode or Aperture Priority. This allows you to manually adjust the aperture, while the camera automatically adjusts the shutter speed. This also allows you to adjust the depth of field based on your aperture setting. What you are changing manually is the "F stop". The lower the F stop number, the larger the aperture or opening which lets in more light and also creates a shorter depth of field or "in focus" area. With more light entering the camera, it then can, depending on the amount of light available, automatically speed up the shutter speed. The higher the F stop setting, the smaller the aperture and the opposite results. It's finding the ideal setting for your desired effect that takes some practice to master (not that I have).
I also do occasionally alter the exposure bias down a click or two due the the intense lighting and resulting contrast in the tank. This results in a slightly darker image but some slight Photoshop manipulations can allow you to brighten up the darker areas while keeping the originally bright areas intact. "Blown out" bright areas are often encountered and I have found this post shot adjustment, done judiciously, to be helpful on occasion. There seems to be better results when you brighten darker areas rather than attempting to darken brighter, washed out areas.
Last of all, every shot determines whether I shoot in manual or automatic focus mode. Typically though, my coral shots are manually done. I also shoot most often with a tripod and a remote shutter control for steadiness. This alone can make a huge difference in the quality of images.
Here's a chart of all the pertinent settings of this last series of photos. It may be easier print it and then go back to the photos for reference. The photo numbers on the chart coincide with the photos from the top to bottom. I hope this helps and thanks for the kind words.
Joseph.