Should I pay with my personal Apple ID account?
Unfortunately, Apple does not yet allow you to have both a company and personal credit card associated with your Apple ID account.
We recommend purchasing a subscription from the web interface using a company credit card instead of purchasing using your personal Apple ID account.
Just sign in then click “Subscription” in the left hand main menu.

If you are already paying using your Apple ID and want to use a company credit card, please follow this tutorial.