Hi Mike.
Yes, I shoot in RAW. My lights are a high color temperature (20,000K) and it's much easier for me to get colors right shooting in RAW and setting the color temp in software (I use Photoshop Elements but there are lots of programs one can use).
I do all the usual things you hear about - clean your glass inside and out, turn off all pumps, use a tripod and shoot straight through the glass. Shooting perpendicular to the glass is very important for clear, undistorted images. A novice with a point and shoot shooting straight through the glass is more likely to get a better picture than an expert with a high dollar dSLR and lens shooting at an angle through the glass.
An implication of this limitation is that in order to reframe a shot slightly left or right, you can't just turn the camera. You have to move the tripod in order to maintain a perpendicular aspect to the glass. Often times my lenshood is very close to or pressed up against the glass and noticing the gap between the hood and the glass around the lens circumference is another way to gauge how straight on one is shooting.
I usually set the camera to Av mode and lens to manual focus. I start with ISO 100 and try to use that if I can, which is much of the time shooting stationary objects like corals.
Sometimes the subject needs to be moved or "posed" for decent results.
These days I've been remote shooting with live view, meaning my camera is attached to my laptop via usb and I control the camera from my laptop (except for focus, which is manual). Live view locks up the mirror and allows me to see on the laptop screen or camera back (the 50D has an awesome display b.t.w.) what the image sensor sees.
If the subject is changing its distance from the camera or autofocus is required, live view is useless. But for shooting relatively stationary corals, it's custom designed for my needs.
I set the focal plane manually. When I'm really trying to be specific with where the focal plane is placed, I'll use the closeup or magnified view which can be very helpful.
My usual goal with macro photography is to have as much as the subject in focus as possible with a pleasantly vague background. I'll start around f11 or 13 if I can but it all depends on the scene, subject and lighting. And sometimes nice results can be had going as open as f2.8, again depending on subject and composition.
With no water flow and stationary corals, one can get away with fairly long shutterspeeds, upwards of a second or two. Stopping pulsing Xenia on the other hand requires a shutterspeed at least as fast a 1/80-1/100th. 1/100th may not be fast enough for fish.
Once I've captured the image, I load it into Photoshop Elements where I set the white balance / color temperature and fine tune contrast, brightness and / or sharpness. I save the file as PSD to preserve image quality during my workflow. When I'm happy with the image I'll resize it down for screen display (72dpi, 8-900 pixels at the longest / widest dimension) and save it as jpg.
This is just what I do currently. "There are many ways to skin a cat" and "Your mileage may vary".
Ken