You add a payment by clicking on 'Actions' in the Client record and then 'Add Payment.'
This will bring up the screen below. It pre-populates the 'Account Name' and the date.
I have populated this screen with data as you can see in the image below. You are able to change the date of the payment and so this allows you to add payments retrospectively. You can also change the payment type. The payment type options can be set up under custom lists in TM3 web settings.
Once you click 'Add' it brings up the payment with all its details. You will then need to reconcile the amount against invoices. To find out more on how to do this, read this article.