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You'll want to make sure that you've connected your company file to QuickBooks Payments account so you'll see the option to pay online.
To link through the Customers menu
To link your account through Receive Payments
However, if your account is properly connected, you can try logging out and log back in to your QuickBooks
You can also enter credit card annual and finance charges in QuickBooks. Here's an article for reference: Set up, use, and pay credit card accounts.
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