Hi,
Note that you can also use this plugin:
www.hikashop.com/marketplace/product/109...rder-by-obsidev.html
It allows for purchasing out of stock products.
Note however that the payment is made immediately.
If you don't want to charge for the items immediately, some payment methods have an "instant capture" (authorize.net) / "enable valiadtion mode" (paypal) which will validate the transaction when the customer enters his credit card, but won't capture the money until you validate the transaction in your merchant account.
That's what is often used to charge the money only when you ship the goods.
However, they usually don't allow the possibility to capture a percentage of the transaction first, and then another later. So I don't think you can do exactly what you're talking about, or you'll need to have the customer come back to make a payment again, or you'll have to store the credit card of the customer to be able to charge it a second time. In both case however, that's not a usual workflow and thus will require some plugin coding.