(Question submitted by David)
This is a very broad subject because different engine models have different injection systems that require different actions (we'll also assume the boat is in regular use and not being winterised).
The really short answer is that it depends on what sort of motor it is - so always refer to your owners manual from the manufacturer.
If you're mixing your own fuel mix for a two stroke in your fuel tank (eg. 50:1 or 100:1 fuel mixes), it's a good idea at the end of the day when you're flushing the engine to disconnect the fuel line and run it out of fuel. This way if the fuel evaporates out of the carburettor it doesn't leave the oil in the bowl.
If you don't do this and you've had the fuel evaporate, you'll have more oil build up in the fuel mix than ideal - causing smoke & potentially hard starting when you go to start it next time.
If it's a direct injected, EFI two stroke it's not recommended to run these out of fuel as some of the oil injection components run separate to the fuel system. If you run them out of fuel the oil will still keep injecting into the engine causing it to have extra oil on start up next time, and potentially cause hard starting.
There is no harm in running your motor out of fuel with four strokes engines, but it's not necessary to do in most cases (again, refer to your owners manual).
If it's a carburetted four stroke, you can pretty easily run it out of fuel at the end of the day just as a precaution, although it's not a 'must do' if you're using the boat again regularly.
But if you leave old fuel in your carburettor for long periods (over three months), it can block your carburettor jets & galleries with tarnish build ups - meaning the engine won't run properly on restart.
If it's an EFI four stroke it's not necessary to run them out of fuel as this motor doesn't have carburettors, so there's no risk of blocking the carburettor jets.
In summary - regardless of your engine make/model we always recommend reading your owners manual to make sure you're maintaining it as recommended by the manufacturer. Different brands, models & size engines require different treatment so that is the most reliable source of advice.
If you're in doubt, always go with a 'better safe than sorry' mindset and ask an expert for advice about your specific motor.
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