For instance payment to work, you need to enable the instance payment globally or locally.
For Global Settings, go to woocommerce -> Settings -> RnB Settings -> Display
then you need to enable Show instance payment
For Local Settings, go to product -> Settings -> Display -> Local Settings
then you need to enable Show instance payment
The instance payment with deposit option works mainly for the subtotal, and it has to be at least 1%.
For example, you order an item which has a price is 100$ and it has a deposit of 500$,
so the subtotal is 100$, and the total is 500$.
So as you use 1% as instance payment, so on the checkout page, the customer has to be paid 10$ (1% of subtotal) + 500$ (Deposit) = 510$.