I'd say that the way you are doing it is too difficult, and as you mention, becomes even more difficult with more usage.
I got a new credit card from Chase yesterday. I created a new account called "Chase Visa". Within about 15 minutes, I had set it up so that it would download transactions directly from Chase into Quicken. My American Express card is set up exactly the same way, with it being a separate account. Today, I was able to download yesterday's transactions on both cards, along with all the others. I examine each transaction, and categorize it when I accept it. Any transactions that are regular expenses, are automatically categorized by Quicken when the transaction is accepted.
When the bill comes due, I go online to my banks web page, and make the payment electronically from the bank. In Quicken, I reconcile the credit card account, and create a transfer transaction from the checking account, to the credit card account. I cut-and-paste the online transaction code that the bank web page provides to the comment section, so that I have a record of the payment transaction. A day or so later, when I download from my checking account, I see the
It mirrors the real world, and makes it very easy to manage the multiple accounts that I have. Like you, I use my credit cards for almost all purchases. With 3% back on Chase, and 5% back on Discover gas card, it doesn't make sense to pay cash for anything.