Rick is spot on about diagnosing the problem. There is no difference between the principals of digital photos and film work, so any older references or books will help.
The best tricks I have learned is to use a tripod and dont use your flash. Most of the time the flash will bounce off the glass or will make everything washed out. Without the flash (shooting in auto mode) the shutter speed will typically slow down, so that is where the tripod comes into play. Slower shutter speeds and shaky hands = blurry photos. It can also help to shut off powerheads to get good coral shots, (so you dont get any blur effect from movement). Fish are always the hardest for me. I cant make them sit still.
The best thing is just to take lots and lots and lots of photos. Eventually you will get it figured out. Try taking a picture of a fixed object and mess with lighting, shutter speed, film exposure and see what effect each one has. If your camera has standard modes like portrait, landscape and macro, try taking the same photo with each setting. That is pretty much what I did, until I found out what worked.