There is no setting in Sage BusinessWorks to specify a Vendor is set to only process checks via EFT.  At the point of invoicing, you can elect to use a Prepaid term and indicate the EFT #.  But the system will treat the invoice as being paid once you post it.  If the invoice is not going to be paid until later, then using the Prepaid term will not work and unfortunately there is no other work around.