Before you update, back up all your iPad, apps and personal data first. Then go through the upgrade feature.
When I did mine last week, iOS 5 upgraded and installed within about 10-15 mins. When it finished all my apps and music had gone. I then did a restore from save. My music and apps didn't come back. So I spent 15 mins or so manually re-syncing or copying my apps and music back over to exactly the way I like it.
Then when I opened all these apps, all my personal data was restored exactly as I'd left it. Every app.