I just did a deposit and when selecting New Deposit, one of the invoice/payments isn't showing up but on the register it shows that it went through?

I will help you with showing your invoice payment on your deposit page, Michelle.   

To view the invoice payments when creating a deposit, make sure these transactions are on the Undeposited Funds account. Otherwise, you’ll need to change the Deposit To into Undeposited funds.

Here's how:

1. Go to My Apps and select Customers under the Customer Hub.
2. Select a customer from the list, then look for a payment transaction in the Transaction list tab.
3. Click View / Edit under the action column.
4. Choose Undeposited Funds in the  Deposit To dropdown.
5. Click Record and Close.
   
   

For visual reference, see the image below.

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