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Hello there, @hanky..
I can provide with additional information on how to record your bill payments.
When you entered a bill in the Enter Bill window, you can use the Pay Bills window to pay that bill. Otherwise, the bill will not be marked as paid. Whereas, you can use the Write Checks window only if the bills have not been entered and you don't need to track them.
On the other hand, paying bills will not affect your inventory nor Cost of Goods Sold. Only the bills that you've entered and item received affects your COGS.
For more insights, you may check these articles:
Let me know if you have other questions. I'm just a few clicks away.