It's often quicker to record payments during the reconcile process. Also if clients purchase from you online, their payment is automatically recorded so no further action would be required, however here are the steps to manually record a payment:

Head to Finances then Payments:

Fill in the information related to the payment and save:
​

Now you'll see the payment in the Payments Received tab, as well as the Transactions area.

 
​Related articles:
​How to check your client balances
​How to send payment receipts to clients
​How to create and send client invoices
​How to record and track expenses