It'd be my pleasure to help you with payments, tag31161.
When you apply a payment to a bill, the bill status will automatically change to Paid. You may check this article as your reference: How to enter and pay bills.
If you're referring to the payments for invoices, Paid status on an invoice means you already processed payment. Every time you processed payment, there'll be a new Closed payment transaction. This means, a Paid status is only for invoices, not for the payment. See this article for reference: How to record a customer payment.
I'm always here if you need anything else. You can reply to this thread anytime.