There is no easy way to do this using the built-in functions. However, there are several ways to achieve this:
- Create a promo code / discount, for example, 90% of the order (leave the "code" blank and it will be automatically applied to all orders). In your template, make it clear that the discounted amount is a “deposit” and that you will ask for the remainder later.
- Write a PHP extension to calculate your deposit and update your basket at checkout.
With the first option, there is no easy / automatic way to request the remainder of the order (since the Store believes that it is already fully paid).
The most flexible option is to write a simple extension to require only a deposit during the checkout, and once the order is created, you can also use the standard functions to require the rest of the payment (your customers will still need to re-enter their credit card details, since they are not saved).