To apply a retainer or an advanced payment, you need to go to the Payments screen, set the payment method to Use Retainer, then enter everything else just as you would for any regular payment. You can see the available retainer also on this screen. Check CORE Help Center for details.
If you are unable to use a retainer in CORE, the reason could be that you are using the wrong payment method. You must select the Use Retainer option in the Payments screen to apply the retainer to the invoices.