A bill records something received before the vendor is paid. Select the vendor, bill date, reference number and due date, then classify the lines. A bill can debit an expense or an asset: equipment does not become an expense simply because it arrived on a vendor invoice. The credit is Accounts Payable.
Pay Bills settles an existing payable. Select the bill and the actual bank account, then enter the amount being paid. A partial payment leaves an open balance. Do not record a second expense or check category for the same cost after entering the bill. One bank payment may settle several bills from the same vendor, but the allocation should remain visible in the vendor history.