It *should* go fine with the Full Upgrade option. I personally don't do upgrades, the one time I did one(Dapper to Edgy), it felt like my machine was going through water and was slower than when using Dapper. So I did a clean install of Edgy, and it ran perfectly. Since then, clean installs for me. I keep a pretty current backup of all my files, etc, along with a .txt file that has odd settings for all of my programs, in case I have trouble remembering how I had set a particular program. I can remove Linux, reinstall, and have all of my files transferred back and all my preferred software installed and setup, in about 90min.
Just to be safe though, make sure you have a current backup of all important files, etc. Will something go wrong? Probably not. Could something go wrong? Definitely.