I have a D7000, Nauticam housing, two Ike 160 strobes, a sola focus light and wide angle, midrange zoom and macro lenses.
I always shoot in RAW. RAW allows for penalty free adjustment of white balance in post processing.
I always shoot manual. I do not like the auto settings like aperture or shutter priority because the camera can put you into an inappropriate setting.
I tend to run a shutter speed of 1/200. I generally stick with this but I will slow it down sometimes.
i shoot an aperture of F 8. If I increase the aperture, I lose some resolution because of diffraction. On macro shots, depth of field can take priority and I will bump up the F stop to up to 20.
i will vary ISO according to the light. The D7000 performs well at high ISO and I will bump it up to 1000. Generally, I like being at 200-400. On macro shots on sand, I find ISO 100 is a must and I often wish I had an ISO of 50.
I pay close attention to the histogram. I try to expose to the right meaning the mode is in the right half, if possible. Histograms can cause some problems because they are usually background dominated. It is more important to properly expose the subject.
i have a couple of suggestions. See if you can pick up a good used 60 mm macro with auto focus and internal focus, meaning the lens length is constant while you focus. The 60 macro is a great lens and very useful underwater.
My other suggestion is to get Martin Edge's superb book on underwater photography. It is the best treatment of the subject that I have seen.
---------- Post added December 29th, 2013 at 12:20 PM ----------
By the way, I have learned to do a ranging shot or two or three to get the exposure right on a subject before I move in for the critical work on focusing and composition. I have heard of photographers spending a long time on a single subject. I talked to one guy who spent something like 40 minutes waiting for a frog fish to do something. He got a shot of it grabbing a fish.
The more experienced I get, the more time I spend with individual subjects.
