Invoices can be paid by clients in several ways.
By Credit Card (through Stripe)
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
And... you are done!
Nice work, your clients account is now up to date.