A lot of different questions in there, I will try to answer them one by one.
Are ship engines made to go 100% most of the time?
Ship's engines have a rated called MCR (maximum continuous rating) and they are designed to be capable of running at this power indefinitely, but owners / operators often choose to run the engines at lower power either to suit schedules or to save on fuel. On some engines if you want to run them at very low power ratings then it is necessary to fit different injector nozzles and sometimes even to blank off a turbocharger.
Can they change quickly from full to half to stop to reverse?
Engines tend to have a manoeuvring range in which they can be easily stopped and started without causing too much thermal stress, depending on the size of the engine this is normally about 40-50% power output, when arriving into a port, the engine would usually be slowed gradually to manoeuvring speed and then it would be operated as required by the bridge, outside of these manoeuvring speeds the power output would be changed gradually (often by a load control program) unless an emergency situation requires a sudden change.
On long voyages do they run continuously at full power most of the time?
As above this depends on many factors, they can run on max power all the time, and in my experience run better at high loads), but for various reasons they are often run at low power settings. When I have had to run the engine at low power outputs, I have always tried to get the captain to speed up for 1 hour every day to clear out any carbon build up.
I've know a few car drivers, especially with new vehicles, who tend to try to vary the speeds to run in the new engines. Would this happen with a ship?
Yes. When a ship is delivered the engine has been through testbed trials in a workshop and sea trials so it is already run in, but when any maintenance is carried out to the cylinder liners or piston rings then the load is increased steadily according to set manufacturers guidelines in order to run in the new piston rings / liners.
My own gut feeling on the sim has been to power at about 80-90% for cruising, saving 100% for emergency runs. Altho I do slam from forward to reverse quite a lot, and also on the two engine setups use the classic one forward and one back for sharp cornering.
I'm curious to know what the real life practice is.
Real life practice varies from captain to captain, those who "slam from forward to reverse quite a lot" (the nautical terms are ahead and astern by the way) tend to feel my wrath rather quickly.
Really the engines should be used as gently as possible in order to maintain the ship in a safe position, but keeping the ship in a safe position has to be the over-riding factor. As for one engine ahead / one astern then this would be common practice when manoeuvring at very low speeds, but not when on passage. Putting the engine astern when the ship is moving ahead at any speed puts a huge load on the engine and risks damage.
Hope that helps clear things up.