Invoices can be paid by clients in several ways.
By Credit Card (through Stripe)
Cash
e-transfer or other payment service
When a client chooses to pay using a method other then Credit Card, here's how to log a payment on a past invoice.
How to create a payment on a past invoice.
From the Invoices tab within a Client Record
Select "Edit" beside the invoice you would like to record a payment
Click "Create Payment"
Select the payment method.
Input the corresponding information for your records
Click "Pay"
And... you are done!
Nice work, your clients account is now up to date.