Again, I'm just getting started setting up a test sync to see if mirrorsync will work for us.  Our app uses what I guess has been termed the "data separation model".   All of our layouts and scripts are in on file1.fmp12 file along with the security (list of users and their privileges).  A second file2.fmp12 file containing all of the data and a single "admin" level user sits alongside the first file.  So the user logs on by launching file1.fmp12 and the relationship tab under "manage database" shows the links to all of the tables in file2.fmp12 with relationships.  

So with all that being said, when I'm setting up mirrorsync, step 1 had me copy and paste tables.  I pasted them into file1.fmp12.   I pasted the scripts also into file1.fmp12.  My intention is now to setup all of the required layouts for the tables being sync'd into file1.fmp12. I thought that before I spend a half hour setting all that up I would ask here if I'm taking the right approach or not.

I appreciate any followup advice on this.

You're doing it right: http://docs.360works.com/index.php/MirrorSync_advanced_topics#Separation_model_.2F_multiple_file_solutions

Wonderful!  Thanks.  I'll read the link you provided.