To process a Motability deal, where an invoice to Motability company is required, to show car purchase only, and where there are some additional accessories purchased by the customer, therefore an invoice to the customer.
You would configure the Finance & Information section of the order process.
The PX deposit value should include the customers contribution and also the value of any additional options.
When the final figure comes in from Motability, the final step would be to discount the metal of the car, and then all will balance off.