In order to pay an instalment, just select it in the Payment window of the user's profile under the Instalments section (the system provides a list of the pending instalments).
Once you have clicked on Pay Now, the selected instalment will disappear from the list.
If you click on Payment, you will see a summary of the amount paid and the amount yet to be paid, as shown in the example below:
You can still create new instalments before closing the final balance (see here)
To pay the final balance, just select the corresponding box and click on Pay Now.
If you click on the plus, a drop-down list will show all the instalments related to the payment