Splitting a direct deposit between two banks for vendors isn't currently offered in QuickBooks Desktop. However, you have the option to change the vendor's bank account while creating and sending a payment.
You can update the vendor's bank account information on the same page that you set it up. Below are the necessary steps to complete the process.
Click Vendors at the top menu bar and choose the Vendor Center.
Double-click the vendor's name to edit his information.
Go to Additional Info and hit Direct Deposit.
To get more details about direct deposit for vendors, check out these articles: