Managing Down Payment on Sales Order

We sell a build-to-order product with 8 weeks lead time.  We require a minimum 20% down payment (exceptions occur, so we must account for variations from 20%) of the full sale price before we begin the build.  Here is the desired workflow:

1. Create Sales Order with full price of product
2. Invoice 20% of the Sales Order amount
3. Customer pays down payment invoice via email pay (secure portal 3rd party)
4. Apply as a Payment/Prepayment on the Sales Order
5. The Payment/Prepayment automatically applies to the final invoice at end of the build

The problem is that I cannot create a down payment invoice for the 20% linked to the Sales Order.  I can send the Sales Order form with an email pay link on it, but it will be for the full amount.  We can tell our customer to only pay a certain amount, but the customer will have to manually modify the amount (because the payment amount for the customer will default to the full sale price).

Is there a workflow to handle down payment invoices?