Hi Justin,
Are the GUID fields populated with values?
The manual process you describe above will only need to be used if child GUID is not populated. For example, say I have the relationship between a feature class called Airports and a table called Districts based on the FCC fields. I can select the airport, and the field in the Districts table that should be related:
I can then right-click on the District value in the Attributes window and choose to Add Selected to Relationship.
After doing so, the FCC field will be updated with the FCC value from the Airports feature class:
If the FCC fields are not populated, there is no way for the relationship to know which features are related without doing this manually.