Email will be sent from any of modules such as Cases, Accounts or Projects in sugarCRM. So Email will be attached with cases,Accounts or Projects in sugar.
If customer replies to this email thread then that particular email also has to attach to the main modules such as Cases, Accounts or Projects.
So we will be able to see all the email conversations related to particular cases,Accounts and Leads in Email subpanel itself.
Assumption : Inbound Email settings are configured for the user.