When I was doing it, I'd balance it at the end of the month comparing the checks I wrote against the statement. Then I'd use Quicken and import the monthly statement and enter in the checks. Was not very efficient but it was nice (=scary) at the end of the year to see where the money was going.
My wife didn't like my system and decided she wanted the joy of checkbook balancing. She does a much better job at it than myself.
That said, in all the years I did it, I never had any serious problems with the bank. A few times there were mistakes but by the time I got to balancing they'd already corrected them. The problems I had were getting the CC checks sent out in time to avoid the late fees. I seemd to get hit 1x/yr by sending it in a few days late. Fortunately they have a forgiveness policy that will waive those fees if you call them, so, I usually got out ok. To this day, although they all claim they do, none of the banks I've spoken too will setup a direct withdrawl to cover the minimum payment each month. I've asked a few times when I switched banks and they said they have it. Then when I get the card, "oh no, I'm terribly sorry, we made a mistake we don't have such a service" or "it's only for a business (or non-business) accounts" blah blah, but we can set you up with this insurance to cover your payment if you are late.
:| Oh well, Ijust send it in on time. But still, sometimes you just get too busy to deal with the bills for a few days, the cc bill came in a few days late, and next thing you know your rushing to the post office hoping it'll get there on time.
And online bill paying = $$$ so I'm not going down that road.