It's one thing to lay up a for the winter, because organic matter doesn't stink in cold weather. But when a boat is likely to sit through summer and winter months, it's advisable to decommission the whole system, because not only is anything left in the tank likely to evaporate and harden into "concrete," but the lines can also permeate with odor, and the animal fats in waste can congeal...sea water minerals can harden, etc. So it's advisable to leave the system as close to 100% pristine as possible if you don't want to come back to major problems. And if you're in a climate where winterizing is necessary, it would be advisable to winterize too.
Flush the whole system VERY thoroughly with clean fresh water. After pumping the waste out of the tank, add a few gallons--enough to cover any sludge--through the pumpout fitting (because that sends the water into the tank at the bottom to stir up any sludge), pump out...repeat...repeat...till you're pumping out only clean water. Fill the tank with water and low suds detergent--NO bleach or other chemicals!!--down the toilet and the pumpout to clean out the hoses. If possible, take the boat out and tack a lot to agitate the solution. Add more water so that the detergent solution overflows out the vent to clean it too...and let it flow for a bit. If you have a pump to dump the tank at sea, use it to dump the detergent solution so that you clean out that line and the pump too, or pump it out...give the whole system including any overboard discharge pump and lines, a final rinse with fresh water down the pumpout hose and the toilet...empty that...and finally, lubricate the toilet, seacocks and any other pumps and then winterize, or not, as needed.
That will keep your whole system clean and ready to use months or even years from now.
It would also be advisable to decommission your fresh water system too...leave that system as bone dry as possible.
<hr width=100% size=1>Peggie Hall
Specializing in marine sanitation since 1987