Hello,
If you enter a bill and put the invoice number in the Ref. field (under the date) it will notify you of duplicate #'s IF it is set up in preferences to do so.
If you enter a bill then just write a check to pay it INSTEAD of going to the Pay Bills window, the bill will not be shown as paid, but you will have a credit for that vendor which you can apply to in the Pay Bills window.
You can pay bills just by writing a check but then you will not be able to use the "warn when using duplicate bills" feature.
Entering bills, then paying bills is the best way to handle A/P. However, if you have a small operation, then it’s ok to take the shortcut as I have in the past for some companies, and others I went detailed all the way.