Regarding the initial question, if sanitation hoses have permeated the only way to get rid of the odor they give off is to replace the hoses. The way to check is to take a damp rag, wipe it along the hose, and smell the rag. If it has a sewage smell, the hose is permeated and the only cure is to change it. The fact the hoses on your boat were changed "years ago" could mean they have permeated, depending on the type of hose that was used.
The "dying salt water" smell that develops in stagnant seawater standing in the toilet intake line up to the boat's water level can be a major source of smell when the toilet is flushed. I don't know of a cure for this. We keep the intake seacocks for our two heads closed unless we're going to be using the toilets. When it's just the two of us we use the aft toilet almost exclusively.
We have never had an odor problem from standing seawater in the aft head plumbing but we do in the forward head if we leave seawater standing in the intake hose for a week or more. Not a problem on a cruise when people are using it regularly. Fortunately the forward sink drains to the toilet intake seacock so unless we have guests we just leave the seacock closed most of the time and if we use the forward toilet we run fresh water into the sink and then pump it through the toilet via the sink drain line.
Regarding the question about how often an engine should be run during periods of disuse in the winter, our policy is to run the engines in the slip if we don't take the boat out for a month or six weeks maximum. However letting them idle is almost as bad for them as not running them. Worse, actually. The engines will never reach operating temperature at idle so combustion will never be complete in the cylinders.
We start our engines, let them warm up for a few minutes, and then put the transmission in forward and run the engine on up to about 1200 rpm. We let it run this way under a load until the engines reach operating temperature and then we run them a little longer before shutting them down. This typically takes about 30-40 minutes. We do each engine separately to reduce the strain on the docklines. We used to do them at the same time with one in forward and one in reverse but I don't like running our transmissions in reverse under power for any length of time so we changed to doing first one engine, then the other one.
But we have friends who rarely run their engines during the winter, or perhaps only every few months, and so far as I know they've not had any problems with this.
We also keep heat in the engine room during the winter so the space is always between 50 and 60 degrees. So the engines start right now even in February, as opposed to cranking for a long time because they're very cold. This makes life a lot easier on the starters I think.
So that's what we do but you'll hear as many theories about what to do with your engines as there are people who'll tell you.
-- Edited by Marin on Wednesday 27th of October 2010 12:34:00 PM