An invoice says you have charged the customer. A payment says the customer has actually paid. Those are related events, but they are not the same event.
Why the distinction matters
If you mark invoices as paid too early, your receivables look cleaner than reality. If you record cash with no link back to the invoice, you lose visibility over what is still outstanding.
What good handling looks like
Raise the invoice first, then record the payment when it arrives, then allocate the payment correctly. That gives you a receivables position you can trust and a cash position that matches the bank.
How it affects reporting
The aged receivables report, cash position, and customer follow-up all depend on this separation being handled cleanly. See the workflow from invoice to payment allocation.
Start with the basics
If your current records blur invoices and payments together, start a workspace and move them into one operational flow.