Hello there, @OC Bookkeeper.
I'm here to help you today so you'll be able to pay your bills correctly.
If you wish to pay your bill with an associated check, you really need to pay your bill #1 and bill #2 individually. If you'll select the two bills together in the Pay Bills window, then, the payments will be combined in 1 check.
You may see attached screenshots for additional reference.
In addition, to learn more about paying bills in QuickBooks Desktop, you may check this article: Pay bills in QuickBooks Desktop.
Please don't hesitate to drop a comment below if you have any other questions about paying bills, I'll be always here to help you. Have a great day ahead!