Hi Michael,
What version of Adagio FX are you running?
The most current version 9.1A allows you to specify specific departments for retrieval, excluding any accounts that do not have selected department codes. The
new release video has a demonstration of this, starting around the 1:48 mark.
If you are running an older version of FX, you have to specifically code the desired departments into an automated retrieval process. These steps are outlined in the Help file, by opening the topic related to Retrieving data and then clicking the link to Auto-Retrieve. If your version of FX is too old, this help topic may not exist for you.