Hi Stonegalleria
From the software's perspective, you can manually create a credit in order to refund a part of the sale, such as a deposit. For more instructions please follow this Help article: Customer returns, credits and refunds. If you are not refunding the payment received, please do check with your accountant on how to account for this payment in your business set up.
You can certainly enter GST only transactions within AccountRight, please follow the steps explained in this Help article- Non-standard GST amounts.
I hope this helps. Please feel free to reach out if you have further questions.