Hello, AndreaJB.

Thanks for getting back to us, and I hope you're doing well. I'd like to take this moment to address your concern about handling those bills from auto-pay vendors. 

QuickBooks has a generalized way of paying the bills. So, on the Pay Bills window, all unpaid bills from vendors would appear. We're unable to filter them out based on how you would want to pay those bills. 

I agree that having those options on a vendor level would simplify the process for your AP person. So, I recommend sending feedback to our developers about this input. 

Go to the Help menu, hover on Send Feedback Online, then select Product Suggestions. 

Our developers would take a look at your inputs and ideas and might consider them for future updates. 

If I would also suggest, we can indicate on the bill Memo field that the vendor is on auto-pay (or ACH, depending on your payment).

Then, the AP person would pull up the Unpaid Bills Detail report to determine which bills are meant for ACH or not. 

Afterward, they would pull up the Bill Pay window then check and pay those bills. 

We just need to make sure to add the Memo column to the report. Simply click on the Customize Report button, then search for Memo under Columns and check it. Hit OK to apply the settings. 

Need help reconciling your payments (and other entries) on your bank account in the future? Check out this guide for more details: Reconcile an account in QuickBooks Desktop. 

I'm all ears if you have more questions about managing vendor bills in QuickBooks. Would you like some assistance in managing other entries? Let me know and I'll guide you through.