To add a payment to an invoice, first go to the 'Finances' section of TM3 and search for the invoice you wish to make a payment towards. Then click on the invoice to open it.
Then click on 'Add New Payment' and the following 'Add New Payment' screen will appear.
Enter the details of the payment and then click 'Add' to add the payment to the invoice.
You will be directed back to the invoice, where you will see the payment noted below the amount owed.
If there is still an outstanding amount it will appear in the table on the bottom left hand side of the invoice screen.