While the way you have setup for your organization is good, I don't think you will have a hard time learning a new way. Plus, when you plug the recorder into your computer, you can rename the files as you wish as you move them into the correct directories. I know this is not ideal but i think the m10 is a recorder that deserves a hard look even with this negative point.
For binaural mic recordings, take a look at countryman b3. I have a pair of omni mics that could be used in a binaural fashion and don't require a pre-amp.While they are more expensive than binaural mics on soundprofessionals, I think the quality is also better.