When you've made a Stripe payment, you should record the payment as Card.
In the Web Portal go to CRM > Invoices > edit pen for the invoice > scroll to Payment Details > enter amount paid > select Card > select Record Payment > select $ Add Payment.
If you are taking the payment electronically through Formitize, select Take Payment instead of Record Payment > enter card details > select $ Add Payment.
In the App go to Accounts > Invoices > swipe left on the invoice > select Take Payment > enter amount paid > select Card > select Record Payment > select Add Payment.
If taking the payment electronically, select Take Payment > enter card details > select Add Payment.