EFT Child Support Bank Transit Number

We are in the process of setting up EFT Child Support payments.  For our organization the bank transit number for EFT transactions is different than the one for checks.  The EFT file used the Value of the Transit Number field from the G/L bank account in Bank Account Information.  I can't change the value to the EFT transit number as my checks will then have the wrong transit number.  Has anyone else experienced this issue?  Does anyone have a solution?  We are thinking the data may need to be manipulated/corrected before transmission to the bank, but this is a less