Do you have your credit card accounts set up as "on budget" accounts? Thats the default option. In that case, when you make a payment to a credit card, you set the payee as "Transfer to [cc account name]". A corresponding deposit transaction will automatically be created in the credit card account. If you manually entered or imported a payment transaction, match it with the auto created one.

Do the same thing when transferring money between any other accounts...don't assign a category to it, change the payee to "transfer to ..."

I'll try to respond more later, my kid just got out of bed....