[MorganPaul]

I have done it many times. Remove the hose that goes to the threw hull, put the hose into a 5 gal bucket of water. The bucket should be down at about the same level as the engine. And keep the bucket from going empty by constantly feeding fresh water into it.

 

[MorganPaul]

Very important! Do not crank the engine with the hose in the bucket of water or you risk getting water in places it shouldn't be (the cylinders, specifically). When the engine catches, THEN place the hose into the bucket.

That indeed is good advice.
And I would not put the engine in gear. Make sure it is in neutral.

 

[MorganPaul]

Why would this cause any problem? When the boat is in the water, isn't that like having the hose in the bucket?

How does the water get into the cylinders from the cooling system?

Here is a quote from Don Moyer. Found here:

Much much water in Atomic 4 [Archive] - Moyer Marine Atomic 4 Community

1) The most common way for water to get into the cylinders of an Atomic 4 is for cooling water to back up within the exhaust system by over-cranking the engine with the raw water through-hull open. Without the engine running and producing exhaust pressure to move the cooling water out through the exhaust system, water will continue to collect within the system until it reaches a level that enables it to flow back into the manifold. From there, the water has a direct pathway back into the combustion chambers.