First, find the proposal you want to apply a payment to under Proposals in your dashboard, and click Manage.
After getting in to the proposal, scroll down to the very bottom of the page and click Add Payment. Choose the payment method, enter the amount and click Done.
Adding a Deposit
This payment menu can also be used to add an initial payment or deposit on a proposal.
The proposal will track the amount paid toward the final bill, and the amount remaining. In this way you can add a nonrefundable deposit as a "credit" toward the final bill.