How to account for a payment against an "advance invoice"?


I work with public clients and it is mandatory to have an invoice to receive a payment.

My case is:

  • 1 Sales Order of 10 000€
  • 1 Sales Invoice of 5 000€ NOT linked to this SO (created by Customer>New Sales Invoice

Today, I will save the 5000€ payment against the SO (SO>Make>Payment). Then when I do SO>Make>Invoice, I will have Advance Payment=5000€ and Outstanding Amount=5000€.

The only issue is that the payment is not saved against my initial Sales Invoice, and it has a status “overdue”.

Should I enter 2 payments? (one against SO and one against SINV)
Or is there a way of telling that one payment is accountable for both SO and SINV?

I would be interested in this answer as well. In my case, payment already entered into ERP. For a future invoice, how do I link Sales invoice to payment already entered? Currently, it shows overdue.