Navigate to Sales > Invoices and select the Batch Payments button. By selecting this button you will be taken into an Add Payments screen where you can filter your systems invoices by customer, then record multiple payments with ease by selecting the payment mode, giving the transaction a unique ID, then noting the amount received and then selecting Apply to record the batch payments. 
Note: If desired within this screen you can select the “Do not send invoice payment recorded email to customer contacts”.