Hello there, mhandlon.

Thanks for taking the time to reach out to us. Allow me to address your concern, so let me get this straightened out.

Currently, QuickBooks Online doesn't have an option to deduct discounts automatically on a Bill Payment. What you can do is to process a Vendor Credit then apply it when paying bills. This way, you can record the discount provided by the vendor.

To learn more about vendor credits, you can check this article: Manage vendor credits. 

Since the option you're looking for is not available, I encourage you to send feedback directly to our product engineers for future updates. They place a lot of value in the ideas provided by users, like yourself, when deciding on how best to improve QuickBooks.

Here's how you can send feedback: 

1. Click the Gear Icon.
2. Select Feedback. 
3. Click Next and choose Feedback under Category option.
4. Select Save. 

If you need further assistance with the steps for vendor credit process, I recommend calling our QuickBooks Online Support Team. They have additional tools to pull up your account and do a screen share.

Here's how you can contact our phone support: 

1. Go to: Get help with QuickBooks Online.
2. Click the contact us link. 
3. Select the Search for something else, and type-in Customer Support. 
4. Click Search.
5. Scroll-down and click Get Phone Number. 

Please know that you're always welcome to post again if you have any other concerns. We're always here to help you out. Have a good one.