Thanks for getting back to us, Davvyboy,
Allow me to chime into this conversation and share some insights about recording your customer payments.
At this time, creating a payment deposit towards the A/R account does not automatically tag an invoice as paid. What you need to do is to first link the deposit to the invoice through the Receive Payment option. Check out this article to know more about linking deposits to invoice: How to link a deposit to an invoice
Also, deposit transactions does not have custom transaction numbers. You can, however, use Sales Receipts instead of deposits to record your customer payments with receipt numbers. Just make sure you're using the Undeposited Funds account for you to deposit the payments together. Please see screenshot below:
Lastly, to print your payments, please follow the steps below:
That should do it, Davvyboy. Please let me know if you need further help with your customer payments. I'm here to lend you a hand anytime. Have a great day!