Thank you for posting here in the Community, @camckay1.
You can process a Bank Deposit to record your transactions. Let me guide you how.
Once done, link the deposit to the customer's invoice.
I recommend seeking help from your accountant on how to record the payment of the 13k-worth invoice. This way, he/she can give you the best advice and make sure your books are correct.
Feel free to leave a comment below if you have any other concerns.