Mark overdue invoice (Sales, Purchase and Expense) as paid

1. Go Sales menu, click on Sales Invoice

2. Tick the small box on the left of invoice you want to mark as paid

3. Click at the down arrow button, Click Set as Paid

4. Choose Payment Date and Payment Method, Click Save

OR

You have alternate option to make payment

1. Click to Edit the invoice 
2. Go to payment tab on the left

3. Enter the payment transaction in Payment Received Table, Click Save