You probably want to fog those motors before putting it away for the season. You will need to put a few more gallons of treated fuel in there, enough to do the winterization/fogging. (Be sure you know how to fog a fuel injected engine correctly, by filling the fuel/water separator 1/2 full of 2-stroke oil, NOT by spraying fogging oil down the throttle body.)
Be aware though, that running the last bit of fuel out of your tank sucked all the sediment and crap that is floating and suspended in your tank into the fuel filter and/or fuel water separator. It is advisable to change them out for safety's sake. I'd do this now on that motor that ran dry, and run the fresh 5 gallons or so of fuel through it while winterizing. If anything made it into/past them, I'd want to make sure that crap was not going to stay there for the winter to create more havoc.
Running a gasoline 4-stroke engine out of gas is not too terrible. Doing so with a 2-stoke is definitely not good. Doing so with a diesel is also not good, but mainly because they are so hard to start dry.