Just putting in my 2 cents..
Per Project Folders rocks!!!!
Why would you use it? Well, if you don't, all your audio gets stored in your audio data folder (where it might be if you don't know about it), so if you leave your defaults and format your OS disk you loose all audio... saving as a bundle file can corrupt, which means you have to rename it to wav and line it all up again.. per project folder, all the files in one location, and if anything corrupts it would only be one track or the mix..
Daniel