Our Deposit app can help you take Automated Partial Payment for the use-case where you want to take X% deposit now and Y% later - also in this case the remaining balance payment would be charged automatically.
You can set this up in two steps, by heading over to:
Depo > Settings > Store Flow > Select 'Automated Partial Payment Flow' > Save.
Then you head over to Depo > Products > Manage and you can setup the deposit configuration for individual products.
Currently, the setting could only be set up for specific product(and also the Deposit options shows up on the product page) and cannot be set up to work for all products(On order level, in the cart page) which is why it will only show up for products.
We have also added a short self-help video below that would help you setup Automated Partial Payment for products in your store: