Songbird has been a great piece of software for syncing music onto multiple devices.
However, it shits me to no end when I put in a new device and it syncs the files into the root folder, making an absolute mess and mixing all the (potentially) system folders up with lots of music folders.
If this has happened to you already, I'm sorry but you'll just have to manually dig through and move them yourself.
To prevent it from misbehaving like that, simply make a folder called "Music" in the root folder before syncing.
This will be used instead of the root folder.