You can have a credit card / debit card on file and an Apple Account balance.
If you have set your Apple Account balance as your default payment method, your default payment method will be used first by Apple when you need to make a payment.
If your Apple Account balance is not sufficient, Apple will charge part of the payment from your credit card.
Some purchases might require you to have a credit card on file, even if you use your Apple Account balance to make the purchase.
If you have 2 CC, and you have set one CC as your default payment method that will be charge by Apple.