Good morning, @Alimerraj. 

Welcome to the Community! 

When trying to pay the bill through credit card, are you able to see a field called "Payment No?" If so, this is where you'll enter the reference number. 

If not, please send me screenshot of the page you're on when paying the bill so that we can determine the next steps for you and your business. 

Review this guide for more details on how to pay bills in QuickBooks Desktop. 

I'll be waiting for your response!