Hi there, @speritz.
Thanks for taking the time in reaching out to us. Let me address your concern about the Memo field not printing on your check when processing a bill payment.
To display the reference number when printing bills, you'll need to fill in the Bill number box when creating a bill. This allows you to enter words that can be the substitute of the memo field upon printing the bill.
Let me show you how:
I've added some screenshots below to guide you through the steps:
Also, the memo may or may not print depending on where it was originally entered. Since it was entered using Bills, the memo field won't appear on printed bill payments. Here's an article that will provide details about in which specific screen does the Memo field appears in QuickBooks Online: When the memo field will and will not print.
However, you can manually enter the memo on the payment check in order for it to print.
I'd encourage you to submit feedback, which is sent to the Product Development Team for review when determining features to be added in updates. This way, we'll be able to determine how we can improve your QuickBooks experience. You can do this from within QuickBooks Online by selecting the Gear icon and clicking Feedback or by going to the following link: QuickBooks Online Feature Requests.