If I have more round mesh with a subdivision surface modifier on it, should I remove the modifier in the low poly version, or should I apply it and work from there?

I would definitely remove the subsurf for the low poly, since applying it would make the mesh much too dense, unless you really need all that detail. You can also just uncheck the eye and camera icons on the modifier to disable it, so that it'd be easy to get back or preview if you change your mind later.