Magento2 doesn't do this out of the box. If you want to achieve this functionality then you can create a custom payment gateway extension where you can two option PayNow or PayLater.
If they select PayNow you can successfully place the order with the full amount if they select the PayLater then you can create a custom table where you can save quote id and later you can use it when you want.
To create a payment module in magento 2 you can start by magento sample payment gateway module Here. Make your customizations in it but it will be hard to start from zero instead of that you can go with 3rd party modules and customize it. I found one which may help you with the same. Here is the link Milople Partial Payment
Let me know if you thought. If I can help you further in any technical guidance.