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To clarify, the small balance on the one card should come from new charges. You never, ever have to pay credit card interest.
We should mention that you probably only need to optimize your score when you're about to apply for important credit. But it's good to practice it so you'lll know how to do it when the time comes. Once you can see how the fluctuations work and how you can control them, occasional dips will bother you a lot less.
As mentioned, before statements cut, pay down your balances to the desired amount, either zero or a small balance. If you leave a small balance, pay it in full sometime between the time the statement cuts and the due date. Because that balance will be small, you'll probably have no trouble paying it right away. Also keep in mind that if you're micromanaging your statement balances, you might need to give your card a rest from any new charges around statement time as you can't be sure when pending transactions will clear.
If your cards happen to be with Chase or US Bank, let us know, and we can fill you in on the quirks involved with them. It's no big deal; they just behave a little differently.
Also, if you feel that you need to restore the points that you lost from paying off your loans, take a look at the first three posts in this thread:
Adding an installment loan -- the Share Secure technique
What you do is open a $500 savings account at Alliant, use it to secure a $500 loan, use the savings account to pay the loan down to $44 within the first few weeks, and spend the next five years paying off the $44. You're only tying up your $500 for a brief period of time, and you'll end up paying about $9 in interest over the five years.