The premium versions of the two plugins are perfectly integrated, let us explain you the process.
The customer will add product(s) to the quote as usual, when the quote is created the admin can choose if the customer should pay a deposit.
If the admin decides to add a deposit to the quote, he can set this option from the backend by editing the quote (WooCommerce > Orders).
The admin can enable the option and set a percentage of deposit that will be calculated from the quote total. The customer will see the deposit option when he decides to accept the quote in the frontend.
E.g. if the quote total is 100$ and the admin sets 15% deposit rate, the customer will have to pay only 15$ when the quote is accepted. The other 85$ will have to be paid in a second order (just like the Premium Deposit and Down payments plugin normally works).