I'm here to sort things out with you, jenniejadin. 

The Deposit field on the Invoice page will reduce the total invoice. The deposit is placed in the Undeposited Funds account in which it has not been associated to the actual account yet. We'll have to create a Bank deposit to do that. 

Let me show you how:

1. We can create an invoice or open the existing one. 
2. Enter the invoice's information and an amount on the Deposit field. 
3. You'll see that the invoice Balance Due is reduced by the deposit amount. 
4. Then, click Save and close. 

Let's create a bank deposit to put the funds into the actual bank. 

1. Go to the +New button.
2. Click Bank deposit.
3. Select the correct the bank for the deposit.
4. You'll see that under the Select the payment included in this deposit there's an invoice (deposit) amount.
5. Select on it and click Save and close. 

If you need more help, you can always leave a reply. Take care always!