Well yes by default, including everything you keep on your desktop and my documents folder will be kept on your boot drive (SSD) unless you change it. You absolutely can keep your music and files on your hard disk drive, but in my opinion it would be nicer to be able to utilize my desktop as temp storage for files I have downloaded or am transferring instead of having to keep a shortcut to my other hard drive. I guess you could say it is kind of a convenience thing.
As for your applications you do have the option of choosing where you want them installed. But say you have some games and applications on your SSD and your almost near capacity and a new game comes out, you might want to move one to the HDD to make room. That is where Steam Mover would be handy.