How do I show that that this invoice is paid after the fact? Don't I need to match the Cheque to this now entered Invoice? And how do I do that?
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You don't need use Enter Bill at all, unless the date of the bill and the date of the payment are different, and you are on Accrual Basis for accounting. The Enter Bill process allows you to enter something you do NOT intend to pay until a later date.
You go directly to Write check for Checks, Debit cards, and Cash. You use Enter Credit Card Charge when you bought something and already put it on the charge card.
You don't have to enter Bills after the fact, in nearly all cases. If you are Prepaying supplies, that is tracked as an Other Asset and applied to the bill, later.
"I notice that when I'm entering the bill and selecting it to pay without printing a cheque, it now sits waiting for me to print. So every time I try to pay a different bill for a different vendor, I have to uncheck those sitting waiting for cheque to be printed."
That is because you are confusing Not Printing with Not Creating. You Created another check; it just hasn't been printed and is seen in the checking account register. If you also entered your own check previously, you now have that expense entered twice: The detail on the check and the detail on the Bill; plus the Bank has two checks for the same expense.
Never Entered Data Twice, using two different methods.
"Oh okay...I was told by the last person here to do this and it didn't sound correct to me. So now how do I reverse this? Should I just delete what I have entered into QB?"
You simply need to make sure your Expenditure details are on the Check or Credit card, or the Enter Bill. You don't want these details on more than one transaction.
And I don't know if you are a cash or accrual basis entity.
"It should correct itself after i have deleted it right?"
Delete anything you don't need. Confirm everything you are keeping has the right details.