Multiple MySQL Hub --> FileMaker Client

We have a complex MySQL and PHP; multi-tenanted application which we are now looking at syncing to an offline portable FileMaker model.

I have essentially solved every problem thus far and have MirrorSync running properly.  

My challenge is this:  Our main MySQL database works in tandem with a second MySQL database; the second database contains 25 million property records.

The working set of data which needs to be synchronised is a small subset of data from the primary; and a single record from the secondary database into the mobile version of the application which consists of a single FileMaker file with identical tables to that of the primary mysql database and a table identical to that of that of the secondary.

How do sync the two seperate databases in a single configuration?  Or is that even possible.  I could see that I could generate two seperate configurations; and perhaps split the mobile version into two seperate FileMaker files; i'm just wondering if there is a smarter way to go about what I need to achieve.