Credit Card Payments are typically considered as transfers from your bank account to your Credit Card account and are not accounted for in the Cash Flow tool.
If your Credit Card is already linked in the Empower Dashboard, then the individual transactions under that account should be included in the Expense section of the Cash Flow tool. Including the credit card payment in the Expense section as well would result in the double-counting of your credit card expenses.
It also can't be counted as a credit to your credit card account, because then the expense and the positive transfer will cancel each other, giving the impression that the total expense was $0, which is also not true.