Glad to have you here in the Community, @anonEthos.
At this time, QuickBooks Online (QBO) only allows you to choose one option to pay your vendor. It's either through the Bill Pay app or via Direct Deposit (DD).
I know how beneficial for you and your company to have both options available. However, QuickBooks is working as designed.
If your vendor would like to be paid through Direct Deposit, you can consider disconnecting the Bill Pay app. This way, you can proceed with paying your vendor via DD. For more guidance, feel free to check out this article: Pay vendors using Direct Deposit.
Also, when disconnecting apps in the My Apps menu, you'll have to reenter the same information upon reconnecting the app.
I'm adding this article to learn more about Online Bill Pay: What is Online Bill Pay?
Please feel free to visit our Community forums again if you have other questions with QuickBooks Online. I'm always here to help. Have a wonderful day!