Hi Jmryan,
Thanks for reaching out to the Community for support. I'll be happy to share more info about receiving and entering a GST refund cheque.
If you file your return using the correct process, QB would have to create an A/R for the Receiver General. You'd need to got the Receive Payments window, choose the Receiver General and enter the amount. Here's a helpful article with more info on filing sales tax in QB.
In case you need further assistance, you're more than welcome to contact our support team. Feel free to ask questions. I'm here to help.