It sounds as though you are using notes for recording details of all customer interaction, including phone calls and appointments. That's not the purpose of the notes feature, but that is the purpose of the activities feature. CRM has different types of activities -- phone call, appointments, e-mail messages, etc. -- and these can be scheduled and then completed.
You might be using notes because they are unstructured and slightly faster than using real activity records. But the downside is -- as you have discovered -- is that you can't track email messages into the notes area so you end up with customer interactions tracked in different places.
I'd recommend that you use the activity management features of CRM rather than using notes.