When you process the first transaction of the credit card payment,
set the category as a transfer to the other ( credit card or bank
account), or use the equivalent "SPECIAL Credit Card Payment"
category. When you process the second transaction, Money should
match it. Be careful to not just Accept if Money did not find the
match on its own for some reason. Click Change and match it to the
transfer you already made if Money did not match it for you. I
would consider this the classic of the ways I like. Note that for
this you would *not* use the Money "EXPENSE Credit Card Payment".
I would Delete that category.
For existing transactions that are already accepted, convert one to
a Transfer and Void/Delete the other.
If you don't see the SPECIAL Transfer category at the bottom of the
list, switch to advanced register. One way is
Tools->Settings->AccountSettings->DisplayAllAccountsInTheAdvancedRegister
The above presumes you download credit card and bank statements. If you are just entering the transaction by hand, just make the payment a Transfer to the Credit card account from the Checking account.