On board a ship, marine toilets are to as "the head." Marine toilets are made in manual or electric vacuum flush styles. On most pleasure boats, the head flushes to a holding tank, which has to be pumped out when full. Many boats also have a "Y-valve," which when flipped bypasses the holding tank for direct overboard discharge. It is only legal to discharge sewage overboard when more than 3 miles offshore, so before flushing your marine head make sure that the Y-valve is directed towards the holding tank.
Before using the toilet, turn the handle to "Wet" and pump a small amount of water into the bowl.
After using the toilet, add ample water to rinse the bowl and lines. (Note: Some manual toilets have a foot pump that draws saltwater in, rather than a "Wet" setting.)
Turn the handle to the "Dry" setting or use the manual handle to pump the bowl empty. Remember to close the through-hull after using the head to prevent seawater from flowing back through the lines and filling the head while the boat is in motion.
It is difficult to avoid the unpleasant smell associated with marine toilets, which comes from organic matter dying in the saltwater hoses. Most boaters keep a bottle of air freshener to spritz after flushing, but using a generous amount of water (or switching to fresh water from the sink) when you flush will also cut down on the smell.
Unlike household toilets, marine heads are delicate machines. The best practice is not to flush any solids "that you didn't eat" through a marine head--this includes toilet paper, feminine products, hair from hairbrushes, etc. If you don't like disposing of toilet paper in a separate garbage can, it is wise to invest in marine-grade toilet paper that is very thin and quick to disintegrate.