I am implementing an email feature into my solution. I have created a separate file based on the Personal Mail example file that comes with the MailIt plugin from Dacons. My question is must the relationships to the tables be made in the source file or to the table occurrences brought over into the UI file, or both?

If you need to make any fields requiring the relationships, then yes in the 'data' file. I try to avoid these kinds of fields (calculated most likely) and use scripted set field. Otherwise your relationships occur where the scripting and layouts occur (the UI file).