Hi Shankar,
SO28 is the Tcode where we map the internet email address (non CRM) to CRM business object. This is important so that once the Email enter CRM, CRM should be able to identify it as a business object. SO28 setting does that. Inside CRM, the mapped Email address (business object) is referred for all distribution logic etc.
SO50 on the other hand defines the classes which handle various processings wrt to inbound email. Yes you can do the class enhancements and assigned you enhanced classes to control the distribution and Email handling behaviour.
SO28 and SO50 that ways are not linked but both are important for inbound email processing.
Hope this helps.
Regards,
Divya