An empty is basically a thing you use when you need to mark a point in some process, fx if you used a mirror modifier you might want to go further then just using an axis and mark specifically from where you want to mirror your model which an empty could mark. thats just one bad example, but there are many uses for empties and a few examples are mentioned
here
In terms of doing things for amnesia you will never directly need the empties, that means feel free to use them in the creation of your model but dont include it in the export.