To take payment against your invoice, locate it firstly by searching in the 'Invoices' tab of the Invoice section
It will appear with a red 'UNPAID' mark at the top of the invoice.
Scroll down to the bottom of the invoice to the 'PAYMENT' section
Enter in the Type of payment, Account, Reference and Value
....And that's it! If your customer's payment is the full total, the invoice will then be marked with a green 'PAID', or if part-payment, it will remain as a red 'UNPAID' until the total has been fully paid.