Hello,
During the Installation of Symantec Endpoint Protection, the mail port number it asks, is for the email notification purposes. That has nothing to do with Symantec Mail Security for Exchange.
Since you have purchased SBS suite, please download the Symantec Mail Security for Exchange software from the fileconnect website and install the same on your machine.
Symantec Endpoint Protection does not scan the Exchange folders and you may require a Symantec Mail Security for Exchange software to protect those folders.
Hope that helps!!