Yes, that would be the easiest way to do it. If you were going to be switching back and forth you could set up symbolic links to move the saves to a network drive (or local drive both OSes have access to), or a Dropbox folder, etc. With D:OS a couple people reported problems doing that (errors trying to load saves), while some did not; I have not seen this mention either way for the EE.
A folder synchronization program could also work, but to have it be automatic you would need to set up a macro or script to run it after the game exits.
