ONTRAPORT only allows crediting back a complete transaction through the payment gateway.
You can usually do a partial refund in your payment gateway's administration section. If you need to have the net price reflected in the ONTRAPORT reports, and if it is acceptable for your accounting methods, you can then void the original sale in ONTRAPORT and re-enter a new transaction for the net amount of the charge.
In this image we are back-dating a manual transaction for $19.95 after refunding $10 of the original $29.95 sale through the payment gateway administration section. Note we have selected Log a transaction (don't charge card) from the drop down, and have selected None for the invoice template to suppress sending the invoice.
Check with your bookkeeper or accountant regarding using back-dated transactions. If you are in the same accounting period this can be an acceptable method, but is usually best handled using journal entries in your accounting software.