The deposit for a room only reservation is the cost of one night (not sure if they use the first night or an averaged cost if there are different costs for each night).
So for a one night RO reservation your deposit is the full cost of the reservation.
For multiple nights you deposit one night up front and then the balance is due at checkin.
Yes, Disney is happy to take your money, so you can apply a payment toward the remaining nights at any point before you checkin. When we have done this we have always called to do it.
SW