The most common use is to place a Red or Magenta filter over the camera lens and a complementary Green filter over the strobe flash to get a Color Back option. This reduces the Green ambient water color and the daylight color temperature of the flash with its Green filter is canceled back to give the image a normal color balance.
Color filter categories are Color Compensation, (CC filters) and Color Conversion (Red, Blue, Green, and Yellow) filtration and are measured on a Kelvin Scale. Daylight is measured at 5000-5500 degrees Kelvin. The more Blue the higher the Kelvin number and the more Red the lower the Kelvin numbers. Some light is a mixture of only two colors. Florescent lighting commonly is made up of Green and Blue and to correctly adjust for this narrow range a Magenta and Yellow must be mixed together to correct for this light source.
The Blue/Green ambient hue found in some water is better corrected with the Magenta /Yellow combinations where you need to record more Blue than Green. The correct lens strobe combination is a mater of personal taste.
If you are using a digital camera you can color balance underwater to a Grey card exposure. The camera will automatically add the correct filtration (Generally Red filtration) in an attempt to reduce the ambient blue light. If your are using a strobe to flash fill and add color to a subject close to the lens, the Red filtration set up by the cameras color adjustment to the Grey card will be very strong where the strobe light falls on the subject. To correct for the over Redness you need to add a Green filter to the front of the strobe. This is how the MCD Cokin filter holder works. Place the complementary Green filter in the holder and you will reduce the Red compensation provided by the camera. The Ambient light will be Blue reduced buy the camera filtration while the stobe light will look normal (Less Red) due to the addition of the Green filter over the front of the flash tubes. The is called Color Back filtration.
Testing and keeping accurate notes on what you do will help you get close to accurate color balance with the Color Back filter applications.