I am looking to configure auto payment for my clients. Each and every invoice which is generated for client should be auto paid and it should use Quickbook payments.

Hi there,

Welcome to the Community. It's exciting to learn you've set up online payments so you can get paid faster using QuickBooks. Rest assured, I'll be happy to share more info so you can get back to doing what you enjoy the most. 

To get started, it's important to note that when you've complete setting up Online Payments on your account, the option to accept invoice payments using a credit card becomes available to your customers. Here's a helpful article that shows you how to: Take and process Online Payments in QuickBooks Online. Once you've verified with the article, I recommend opening your QB account using a private/incognito browser window and see if the checkboxes appear now. 

Give this a try and let me know how you make out. I'll be on standby.