Take a backup of everything. Files and database and try it. I have used it on heavy modded boards where it did not work. If you just got a few mods it should do just fine, But personally i love the peace it gives me to know that every file is standard after a update. If its just a few simple mods i prefer to reinstall them after the update instead.
Plenty of choices. But remember to take backup of everything. mysqldumper is a great tool for the database backup part.