Your new engine should have a Operator's Maintenance Manual supplied with it. Make sure the person that repowered your boat passes it on to you.
Page 12 of that manual covers Winterising and Laying Up fully. In short is covers
a) Change Engine Oil and Filter b) Fresh Water Cooling System should contain a 50/50 soulution of Antifreeze/Water c) If you are in a cold climate, the raw water circuit must also be protected. (i) Close raw water inlet seacock (ii) Disconnect raw water inlet and place in bucket of 50/50 Antifreeze Water Solution (iii) Start engine (out of gear) and run for 5 to 10 seconds until solution is used and seen at exhaust outlet (iv) Shut off engine and reconnect pipe d) Ensure instrument panel is protected and give key switch a spray with WD40 or equiv. e) Disconnect battery and remove for trickle charging and electrolyte top-up if shore power is available this can be done on boat. f) Fuel tanks should be kept full during lay-up to prevent condensation forming inside the tank. water entering the fuel injection system can cause considerable damage.
If laying up 'on the hard' then it's easier to change engine oil before taking the boat out of the water as warm engine oil id easier to pump than cold.
Technically yes, there is a problem with long term storage of an impeller in an antifreeze solution. My earlier answer was just a reiteration from the owners manual. I should expand on this in a couple of areas.
1) The antifreeze should be a potable type, also know as RV antifreeze. This is a much more acceptable form of antifreeze to use, particularly if you ultimately are going to be flushing it into the waterways.
2) A more beneficial method of winterizing your raw water system is to drain it. This is more time consuming but is the traditional, time proven method. To do this you must open your seacock, then crack the screws on your raw water pump and loosen the front plate. Then remove the plug from the rear of the heat exchanger. this will drain the raw water circuit of the heat exchanger, pump and hoses. Remove the front plate of the raw water pump to gain access to the impeller and smear a film of petroleum jelly (vaseline) on the impeller and rubber 'o'-ring if one is fitted. Then reassemble the raw water pump. Now, you have to ensure the exhaust side of the system is drained. Most water lock type mufflers will be fitted with a drain plug, remove this plug to drain the muffler and any water that may be in the exhaust hoses.