Dear Abhay J,
Create first production version for MRP Run so when you go for MD01/MD02/MD03 then system will take that production version. Lot size you maintain according to the routing. If you have not any fixed lot size then take 999999.
Now when you are calling MFBF BAPI through programme then mention there second production version.
See there is also one way through configuration. You can do it by this also. In configuration you have to maintain selection of BOM during MRP RUN.
Regards,
Saurabh Kumar