How do I prevent payroll from trying to do direct deposit but keep the banking feature active to pay vendors?

I've got your back, @campoclan.

You can deactivate the direct deposit for your payroll and use it only to pay your vendor. To do so, you'll have to turn off the direct deposit on each employee. This way, the option will default to checks every time you run payroll for your employees. Here's how:

1. Open your QuickBooks Desktop company file.
2. Go to the Employees menu, then select Employee Center.
3. Select the employee's name.
4. Click the Payroll Info tab and select Direct Deposit.
5. In the Direct Deposit window, turn off the direct deposit option.
6. Select OK.

You might also want to learn more about managing direct deposits for your vendors. This article will provide you more details about it: Direct deposit for contractors.

The Community forum is always open to help you again if you need further assistance paying direct deposits for your vendors. Have a good one.

I just went to do that. They never had "direct deposit" check marked to begin with. I've never put in any employee's banking information or anything so that option was never clicked. 

Unfortunately the warning about a potentially late payroll is sort of stupid and will come up even if no employees are set up for direct deposit. I don't think there's any setting to change that.