While viewing the invoice from the admin area click on the + Payment button to record a new invoice payment, after you click on the button new view will be shown including the record payment form.
Keep in mind that the + Payment button will be shown only if the user has permissions for payments CREATE, also this button may be disabled in the invoice is with status Paid or Cancelled.
After the payment is recorded the invoice status will be automatically updated based on the total amount. If the full amount is recorded for this invoice, the status will be updated to Paid otherwise will be updated to Partially Paid.
If “Do not send invoice payment recorded email to customer contacts“ is unchecked after payment is recorded email (with PDF payment attachment) will be sent directly to the customer contacts to inform that payment is recorded for this invoice.
To edit the email content go to Setup -> Email Templates -> Invoice Payment Recorded (Sent to customer contacts).
Additionally, the system will send another email (Invoice Payment Recorded (Sent to staff) to invoice sale agent and invoice creator, this email will be sent too when the customer pays the invoice online via an online payment gateway.
Keep in mind if the payment is recorded via the admin area from staff member this (currently logged in) staff member won’t receive an email.