Hi additions
Thank you for your post. Typically credit cards are set up as liability accounts with the account type being Credit Card. I assume it wasn't listed as having the account type of credit card. To remedy that one and have it appear in the lists, go to Accounts>>Accounts lists>>Choose the desired account and update the Account Type field to be Credit Card. Checking what you have process it should be two accounts you'll be needing to record to reconcile, one account at the top and one account below. On the account at the top, it must be the ledger for the bank or credit card which received the money, while at the other account below must be an income account.
You may have a look on this Help Article: Received Money that has detailed information and instructions to assist with this. This will help you reconciled those transactions successfully and avoid getting negative amount.
If you need further help, don't hesitate to start a new post and we'll be happy to assist.
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Cheers,
Shella_A