I've done quite a few upgrades now, using various tools and methods. The best resource for assimilating everything you need to know is this series of video tutorials from Siteground. Siteground Migration Tutorial
They make the process look relatively painless. I recently walked through their step-by-step method and enjoyed the ride! Of course, several bugs have been worked out of JUpgradePro since last time I tried to use it... It works much better now!
Email me about your upgrade tricks, hints and hiccups! Email Candyweb