Venkatesh,
These are TWO different databases with TWO different function. If you check the MySQL you will see TWO ODBC (BOE120CMS & BOE120AUDIT).
For more details you may want to read the BOE XI 3.1 Admin guide
http://help.sap.com/businessobject/product_guides/boexir31SP3/en/xi31_sp3_bip_admin_en.pdf
Also the BOE XI 3.1 Install Guide
http://service.sap.com/~sapidb/011000358700000109832013E/xi31_sp6_bip_inst_win_en.pdf
Regards,
Ajay