Like payments, there is not yet a specific location for marking deposits as received, however while we continue development on proposals we can use the following workaround method to track and update the totals to send to clients.
First make a new line item in the proposal. In the description, write Deposit or something similar so you know its a paid deposit. Next change the quantity to -1 (type the minus symbol and then a 1), and enter the amount of the deposit.
You will see the totals at the bottom of the edit are updated showing an amount less the negative you just added. Now Save the proposal and you can send it out with the correct Amount Remaining reflected in the total.
Note: You still need to process this payment normally, as this is not processing a payment, just record of payment received.