Write Check vs Pay Bill
When to use the "Pay bill" vs "Write check" feature
in QuickBooks
The "Pay Bills" feature should only be used to make a payment for a bill that has been entered using the "Enter Bills" feature in QuickBooks. When bills are entered, they automatically go to the Payable account and as such, the payment must be made using the Pay Bill feature which will deduct that portion from the payable account while also inputting it to the bank register. In other words, the "Enter Bills" and the "Pay Bills" feature work together. You cannot use one without the other. If you do, the vendor balances in the payables account will be incorrect.
Also, if you need to keep track of purchase orders, you should use the "Enter and Pay Bills" option to keep track. QuickBooks is setup to give you much assistance with prompting you about open PO's as well as pre-filling the fields for you. QuickBooks associates the bill with the purchase order (or item receipt) to automatically calculate quantity and cost.
In a nutshell, only use the "Enter Bills" feature for bills that you will not be paying in full all at once or if you need to track purchase orders, and then write check for bills that you are paying in full.