Currently Practice only supports credit card and debit card payments for Packages, Products, Services, and Subscriptions.
With subscriptions, invoices following the first successful payment will auto-charge subsequently.
That being said, sometimes you need to change your invoice payment method options on stripe, to disable options like Apple Pay or Google Pay, or to change the options you offer customers directly through stripe.
To do so, just open stripe and make sure you're logged into the stripe account connected to Practice, then follow along with these pictures: