You'll want to define the payment methods that you accept so that they're available when invoicing customers through WholeCell. Here's how.
Click on 'Settings' on the left side of WholeCell. Then choose 'Invoices' under 'Sales and Processing'. To add a payment method, click on the blue '+' button on the right side.
Add the new method here. For this example I am adding PayPal with instructions that will be sent to the customer on each future invoice:
Click 'Save' and your payment method will appear in the list. It will also now appear as an option to use when sending invoices to customers.