1: Debatch the data into single transactions, then call a stored proc with 3 parms on it, the stored proc updates/inserts the two tables.
2. Let Biztalk convert flat file to XML, then send entire XML block to stored proc, then use OpenXML in stored proc to update multiple tables. I recently learned of a limitation of 8000 bytes to the parm you pass to SQL. There may be a get-around, but it looked confusing.