Dynamics 365 supports folder level tracking of exchange folders using server-side sync. We will go through how this works.
In Outlook, create a new folder or view existing folders:
In Email Configuration Settings, select the checkbox:
Then select Settings->Options->Email->Configure Folder Tracking Rules:
You may see the message:
You will see the window. Select your folder for tracking and the regarding record in Dynamics 365:
Emails in the folder will now automatically be tracked in Dynamics 365: