If you have any finance settlements that need to be cleared on a part exchange, these should be added to the deal in the 'Adjustments' section so they are reflected on the invoice.
Use this method when the part exchange value is equal to or greater than the finance settlement.

The settlement amount will then be included in the invoice totals, showing the finance being cleared against the part exchange.
When the finance settlement is higher than the part exchange value - you can show this in 2 ways, subject to funder requirements.

The difference between the part exchange value and the settlement amount will be treated as negative equity and will be added to the invoice total.
If the funder won't fund the negative equity on the deal and the customer isn't putting in a deposit to clear it, meaning you need to to show it separately - you can add this in as a 'One-Off Product' to allow you to do a top up loan.

If you are purchasing a car direct from the customer that has negative equity on it. You would raise a single invoice for the negative equity. This would then be reconciled in your accounting software.