you can create a new FileMaker table with a "foreign key" that would match a "primary key" in the MySQL table. Then relate the two on the Relationship graph. You cannot create in the MySQL from FileMaker ODBC. But you can add fields to the FM table.
Are you using ESS or are you just using ODBC to import the data? It is easiest to use ESS because you can make table occurrences of the MSSQL tables right in the FileMaker Relationship Graph and then use the primary key field in the MSSQL table as a one-to-one relationship with your native FileMaker table. You can use the join relationship to find non-matching records and add those primary key values in the FileMaker table in a script pretty easy. Likewise, you may want to delete any records in your FileMaker table if they no longer match a record in the MSSQL table.