To settle the invoice there are two ways:

1. Setting invoice through payment

2. Settle it through expense accounts.

Case 1: Setting invoice through payment

Go to Income > Invoices

Step 1: Click on the Invoice for which you want to settle the payment.

Step 2: Click on the Add Payment option on the top right side.

Step 3: Select Deposit to Account from drop down, Received Date, Amount, TDS amount if applicable.

Now Select the Receipt of payment as:

1) Cash - In case the payment is received in Cash
2) Cheque - If the payment is received in Cheque enter the Cheque Number, Bank name, Cheque Date
3) Credit/Debit Card - If via cards please enter Transaction date, Card number, Transaction reference Id
4) Internet Banking - If payment is received through Online Banking, Enter Bank Name, Payment Date, Transaction ID.

The payment receipt will reflect in the Invoice window as shown in the above picture.

Case 2: Settling invoice through expense account:

Go to Income > Invoices

Step 1: Click on the Invoice for which you want to settle the invoice through expense account.

Step 2: Click on the settle invoice option which is at the right side of edit option just like in below picture.

Step 3: Select the account with which you want to settle your invoice, and click on settle

Invoice window will be shown as in the below picture.