Hi Jeff,
If the contact is in the To or the From on the Email, they are considered an "Activity Party." Therefore when you click Track in CRM on an Email, it will show under the contact record of each Activity Party. As Jason suggested, you would then Set Regarding to the opportunity, and the result is the Email would show in both places.
Here is an article you might appreciate.
www.powerobjects.com/.../best-practices-for-tracking-activities-and-notes-in-crm
