Seems like credit card payment is being recorded twice

Let me guide you on how to record the credit card payments correctly, Chris.

But before we start, may I know how you recorded your credit card payment? Technically, if the credit card and bank account you use to pay the credit card expenses are connected, you can record the payment by transfer. To do so, follow the steps outlined below:

1. Go to Expenses from the Expenses tab in the MENU.
2. Select the account you need to transfer the payment from.
3. Select the transaction, then select the Pay down credit card radio button.
4. Select the Transfer account dropdown menu and select the account you want to send the transaction to.
5. Click Confirm.

If you have recorded manually a payment in your operating account, you can exclude it so it won't result in a duplicate payment. To give you more information about this, check out this article for reference: Record Your Payments To Credit Cards In QuickBooks Online.

Additionally, once payments are downloaded, you can match the transactions to what is entered in QuickBooks. I've added this article: Categorize Online Bank Transactions in QuickBooks Online.

Post your comment in the reply below if you have any other concerns when recording credit card payments. I'm always here to help.

If I exclude the transaction from where we paid the CC, the transaction wouldn't pop up on my reconciliation. Right?

That's correct, Chris97277.

Any transactions that are excluded will not appear on your reconciliation. From what I can see, the credit card payment is being recorded once since both associated accounts are connected to QuickBooks Online, and then a second time when you're making the "payment received" entry. 

You may consider reaching out to a member of the QuickBooks Online Support Team as agents have the ability to share your screen and can take a closer look at what's going on. They'll be able to walk you through the steps to get the payment entered once so there won't be any duplicate transactions. Here's how to get in touch with the team:

1. Click the Help (?) button.
2. Select either tab to get started:
  - Assistant: Get quick, personalized answers. Select a suggested option, or type a question or topic you need help with. If you decide you need further help, you can still Talk to a human.
  - Search: Search the QuickBooks Online knowledge base directly, or select Contact Us and choose a way to connect with us:
    a. Start a chat with a support expert.
    b. Get a callback from the next available expert.

The following article provides these steps if you ever need them again in the future: QuickBooks Online Support

Please don't hesitate to reach back out in the comments below if you have any other questions. I'll be here to help in any way that I can.