You can enter externally received payments for the respective contracts as follows:
1) Go to the contract details of the customer concerned and click on "Perform action > capture ext. Payment / Refund".
2) In the opened dialog select the "Payment" tab.
3) Enter the posting text as description (also displayed as such in the financial accounting export) and the amount. In the preview you can see the old and the new account balance.
4) Press "OK" to save the payment.