Why is an amount listed as a payment and again as a deposit on same day ?

Let's make sure to match the deposit to your invoice so payment wouldn't show as doubled on the register, jemarrocco.

If you have added the transaction, you can undo the entry. You can follow the steps below.

1. Go to the Banking tab on the left menu.
2. Select Banking, then look for the account.
3. Click on the Categorized column.
4. Choose the item/transaction, then tap on Undo under Action. I've added this screenshot for your visual reference.

   

And then, you can now match the deposit with the invoice. Please go through this article: Categorize And Match Online Bank Transactions In QuickBooks Online. After matching your bank and credit card statements, you can reconcile your accounts. For your reference, here's an article for additional information: Reconcile An Account In QuickBooks Online.

Fill me in if you need anything else about payments and deposits, I'll be right here to help you anytime.