Hi Smithy2
Thank you for your post. I'd like to extend you a warm welcome to the Community Forum. I hope you find it a valuable resource.
When you make the required payment to the ATO, or receive your refund, you need to record the transaction in MYOB. I'll provide you this Help article, Recording ATO payments and credits, that has detailed information to help you record your GST refund from the ATO.
Additionally, the GST payments and refunds should be put into a separate account which you would normally create. I would recommend to seek assistance from your accountant on creating accounts.
Please feel free to post again I'm happy to assist.
If my response has answered your enquiry please click "Accept as Solution" to assist other users find this information.
Cheers,
Princess