I want to lower the price on a payment. Can I charge part of the payment in the Checkout Portal?

Yes, you need to use the Edit and Charge function. Edit the price fields to the preferred amount and check the order lines that you want to charge. A new order line will be created with the remaining amount that can be charged at a later stage. You can also enter a higher price on a specific order line as long as the total sum does not exceed the original reserved amount.