There are two routes in Clinicminds to register a payment for an outstanding invoice.

The route that most probably the backoffice / finance person will take. Go to Menu -> Finance > Invoices tab and search for the invoice.

By going to the patient overview window find the applicable treatment, go to the payment tab and register the amount paid.

Note: When its regarding a treatment-plan a Quote tab will appear where you will find the invoice to register the payment.
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See yellow lines in the flowchart. This is the final step to register a payment for an outstanding invoice. See the complete flowchart for invoicing treatment or product sales or for invoicing a quote.