I have my bill pay set up based on Category.
I have two of the same issue. I recently had my roof replaced and had to pay half up front and half upon completion. The logical setup on this was two one time bills with different due dates for the same amount, category is “4665 Repairs”. In the same thread, I have two federal tax bills, different dates, different amounts, category is “Federal Tax”.
The Upcoming Bill Payments section either shows the first bill due date and amount twice if it is not checked off as paid, or it shows neither if the first one is marked as paid.