Email to Case Creation in CRM 2013 SP1

We are using CRM 2013 SP1 and implementing a functionality of creating a functionality where the email received are converted to case.

We have a custom entity that captures the Users. We are currently not using any of the CRM OOB entities like Contact, Accounts etc for the same.

We are stuck as the CRM does not resolve the User from the custom entity and hence the logic of creating a case with a known user fails.

Any suggestion that can help without adding that data into CRM OOB entities like Contact etc.