I shoot in manual mode, when you partially press the shutter release you'll see a small meter near the bottom of the viewfinder display (this is also duplicated on the LCD display on the top of the camera), this is your exposure meter. If the bars are to the left, then you need more exposure, if it's to the right then you need less.
More Exposure = Higher ISO
Larger Aperture (smaller number)
Lower Shutter Speed
Less Exposure = Lower ISO
Smaller Aperture (Higher Number)
Faster Shutter Speed
You'll note that these are all related to one another, they all change the exposure, but the 'side effects' are different.
ISO: Changes the size of the picture element that 'sees' light; thus requiring less light to get the same exposure. Side effect: while you'll need less light to get the same effect, at some point you'll be able to see the pixels as 'grain' thus resulting in an image that appears less sharp.
ISO 100-200 is a good base for our purposes, it will maximize the sharpness of the initial image.
Aperture: (otherwise known as f/stop) The higher the number, the smaller the opening and visa versa. Obviously the larger the opening the more light will enter while the shutter is open, thus requiring less exposure time. Side effect: the smaller the opening the greater the depth of field with the lens will be and visa versa. Depth of field refers to the amount of the image that appears to be in sharp focus (from front to rear; ie. depth)
F/22 for most lenses is a good starting point, usually one of the sharpest apertures, however F/32 will give even greater depth of field than F/22, but it will require much more exposure time.
Shutter Speed: The higher the number, the faster the shutter opens and closes to admit light to the sensor, higher speeds can 'freeze' motion, however admit very little light to the sensor. Side effect: the slower the shutter speed the more your subject will tend to blur due to motion (sometimes this can be a desirable effect, usually not in a reef tank though). Also there is a rule of thumb with regards to hand holding your camera (as opposed to tripod mounting), use a shutter speed that is equal to or greater than the reciprocal of the focal length of the lens, or in other words if you're using a lens that is 100mm your shutter speed for hand holding should be equal to or greater than 1/100 sec.
All that being said, for my corals I typically clean the glass very well and wait for the skimmer to grab all the little stuff floating in suspension. Turn off all circulation and wait for all to fall still ...
I set up a baseline on my camera: (tripod mount)
Manual exposure mode
ISO 100
F/22
Shutter Speed of 4 seconds
(Depending on your lighting, your baseline may be different)
observe your meter and see what it is telling you, make adjustments as necessary. Photography is all about playing with all of the settings above to get the settings right for your shooting situation.
Hope this helps ... sorry so long winded.