The enhanced emails plugin allows users to send html-enriched emails and use email themes.
This is highly unlikely to happen. The plugin enhances the way WordPress handles e-mail notifications, but it does it in a unobtrusive way. Basically, it provides a wrapper for wp_mail, which can be used for e-mail notifications. If you did override any pluggable email notification functions, make sure to use eemails_wp_mail instead of wp_mail in order to make use of the plugin functionality.
It's easy - just put your email.php theme file inside your current WP theme directory (if you put it inside wp-content it should work as well, but it's bad practice).
An example email template name looks like this: email-action1-action2. The plugin tries to locate email-action1-action2.php in your theme folder, and if it fails - it tries to use email.php from your theme. If this fails, too, the plugin will use its default email-action1-action2.php template, or if it doesn't exist - just emails.php.