When you create a Deal or an Option, an entry for payment is created in Operations/Customer Payments.
In case of leads created, the entry in Customer Payments is created only after adding arrangements to it.
In order to register a customer payment you will always go to Operations/Customer Payments. If there is no entry in this list, it means that the Deal was fully paid. 

If there are payments to be received, search for the Deal in the list . The list is grouped by Deal codes so you will easily see for what deal you have to receive payment using search options available.
Select the deal, edit and select Receive Payment:

Check the amount and edit it according to the amount paid, select the date of payment, select the type of payment and add Payment Reference (this is optional) and click SAVE.

The payment is now saved.

The details related to Down Payment and Rest Payment amounts and due dates are available in the detailed view of the Customer Payment entry.

The information related to payment processed in Customer Payments  is always displayed on the invoice (amount paid, amount to be paid, due dates, etc.).

For the payment received, an entry is saved in Deals/Accounting having CP for type. You may always check the situation of payments for a Deal in Deals/Accounting.