On spending chart - credit card account payment cancels out checking acct pmnts

On the spending chart, the payments that I put into my credit card accounts are cancelled out by the payment that I put into my checking account register. This has been an issue for years and I've never been able to figure out how to stop this. This means that my spending chart is very inaccurate. Example: I download my checking and credit cards account data into Quicken. My Citi card account has a +$xxx payment towards the balance. In my checking account I have the -$xxx payment that goes to the Citi card. The chart pulls in both, so they cancel each other out to $0.