All the data in the BigFix repository are collected from the managed endpoints. So the BigFix Server does not import data directly from an external source.
Making the files available on the individual endpoints for the agents to pick up is the right way to do it.
To do this, you will need some sort of script or application that queries the BigFix database (or better yet, the SOAP API: http://support.bigfix.com/bes/misc/soapapi.html) and then feeds the data into the other database…