This would be an amazing feature to have. In order to collect a deposit online, we had to book the job and send them the full invoice from that job to make a payment on that invoice, I had to turn on partial payments in my settings before doing this. Then for the deposit to be on the customer and not the invoice, I had to manually unapply the payment from the invoice and apply it to the customer profile. It worked. But it should not have to be this complicated.
