Usually people set this up the other way around. They set up FileMaker to serve as the interface for data stored in the SQL Server tables. An ODBC connection allows you to set up table occurrences in your FileMaker database (Table Occurrences are the "boxes" found in manage | database | relationships) that refer to tables or queries of SQL Server.
Yes, this is how it is usually done but the problem is that the data doesn't exist in the MS SQL Server. Some people were using FileMaker as an excel spreadsheet and just entering in data and it had not connection to a SQL server. Right now i'm looking for a way to export the data to SQL...
As a one time fix or an ongoing procedure?
As a one time fix, you should be able to export the data from FileMaker into a file such as tab, csv, or xml. Then SQL Server should have the means to import from a file of that format. Research the import/data transfer options in SQL Server and pick a file format compatible with it.