DrQ,
Idling a diesel, especially with no load, for "long" periods is definitely a
bad idea. So f
or warm up, start the engine, untie the boat, and leave the dock. Takes about 3 minutes from start to leave. Warm up is continued "under load" at about 1000 rpm or less, until your engine temperature reaches above 120 degrees F. Gradually increase rpm as desired at that point staying below "cruising rpm" (80% WOT) until the engine reaches full temperature.
Coming back to the dock, in most cases you do not need to "cool down" the engine by idling in neutral at the dock as some do. In most situations, you will be operating at greatly reduced rpm when entering the marina, maneuvering into the slip, and finally securing the lines, thus already having "cooled the engine" by operating at a reduced rpm. Shut down as soon as the lines are secured. Also your neighbours will appreciate this.
If you are worried about longer periods where the boat will not be used, first, use the boat!
If not, at least "bump" the engine with the starter monthly to move the impeller so it does not "take a set" (or you could remove the impeller for storage). Alternately, you could run the engine with the boat tied to the dock as suggested by Xsbank, but run it in gear under load, at around 1000 rpm (after a very short idle period) but ensure that you have the boat well secured (assuming you don't have some very large boat), for about 30 minutes to ensure that the engine reaches operating temperatures while under load.
Before starting, always give the engine and room a good pre start check. Look for any signs of a problem, like leaks, disconnected wires, etc. Check the oil level in both engine and transmission. Check the coolant level, the fuel filter for signs of debris or water, the belt(s) for signs of wear and looseness, etc. Open the thru hull for cooling water and check the strainer to ensure it will allow for the free flow of water. Do any other pretrip preparations like turning on electronics, radio, disconnecting electrical power, looking around for potential problems like floatsum in the waterway, traffic, etc.
Start the engine, and check for water flow by looking into the strainer, feeling the raw water pump (it should be cool, not warm or worse yet hot), or watching for it's discharge if that is visible (my boat it is not visible). Cast off as described above.
Underway, keep an eye on your gauges to ensure adequate oil pressure, the alternator is working properly, and you are not overheating. Periodically check the engine visually and by listening to it (for strange new sounds).
I would suggest the installation of a raw water flow alarm to monitor the flow of cooling water. They are not expensive and it will let you know if you forgot to open the thru hull or somehow the seacock got blocked (plastic bag for example). I also suggest adding an oil pan heater to keep the engine warm and to help keep the ER dryer. Inexpensive and only use about 250 watts of power when plugged into shore power.
Like Ken, I change the oil in the fall, don't run my engine or gen set all winter. I store them with freshwater and "salt away" in the raw water cooling system, I run my oil pan heater, and I bump the engines monthly with the starter to avoid allowing a set in the impellers. Never had a problem.