Go to Patient's Dashboard, either through clicking the name on the calendar or in the "Patient Finder" 

Once in their dashboard, you can see their balance in the "Billing" section \
 

Apply any credits in  "Discount Amount:" field.

For check payments, add their check number and amount paid, Click "Save"

It will create a printable invoice/receipt. Click "Show Details" to expand it

I want to cancel the check payment and add a credit card payment instead for demo purposes, so I Click "Undo Checkout"

Click "Yes" to confirm that you want to undo that payment

For credit card transactions, go to "Patient Billing". Note you can use patient billing for your cash and check patient payments as well

Click this dropdown and click "Credit Card".

Check Payment
Cash
Credit Card
Authorize.net

Click "Pay Now" and the payment should go straight to your stripe account. Also, you it will generate the invoice/receipt to give to the patient.

Check and Credit Card Patient Billing