How to upgrade 2.9.2 to 3.2.1 without changing anything internally

I’ve been using wordpress 2.9.2 from since last year. The site is getting a good amount of traffic and their are many links pointing to it. I want to upgrade to the latest 3.2.1 as their is lot of flexibility and it’s more secured, but I am afraid as it might affect the whole structure of permalinks. The menu system is different in newer WordPress so if I update it to the newer version, how will that react. Please guide me as I don’t want to lose the rankings in search engine.