The Pay Deposit option appears only when all of these are true: Allow Partial Payment Percentage is on with a value between 0 and 100, or Allow Fixed Partial Payment is on with an amount greater than 0; and no payment has been recorded on the proposal yet (once a first payment exists, later checkouts always settle the remaining balance). Also make sure you saved the proposal after ticking the option — the values are only stored when the checkbox is on.