How To Receive An Invoice When You Were Paid Less Than The Amount

1. In your Invoice >> click Receive payment >> enter the amount of $500, but make sure that before your hit SAVE, choose UNDEPOSITED FUNDS for the Deposit to drop down arrow.
2. Save that screen as a received payment.
3. That will return you to the main screen, Now, click +NEW icon >> click Bank Deposit >> choose the correct Bank where the money will be deposited >> and then click the Payment of $500. Then, click the ADD FUNDS option below, choose ANY expense Account for the ACCOUNT and enter the amount of -$50, and SAVE.

This took 2.5 hours to verify with some idiot at QuickBooks Help Desk so value it.