Godaddy for some reason requires you to have a primary domain setup for each hosting account. So this basically makes the root whatever the primary domain is.
There is a way that you can setup a false domain so that you can take the previous primary domain and move it. see the link here http://help.godaddy.com/article/4067
This will make the root non-web-accessible. You basically create a false domain of anything you want as long as it isn't used by anyone else. You can then move all your domains to a central area.
For instance my previous setup was this
After the switch I have
/root/falsedomain <--not web accessible as well as any folders at same level
/root/sites/site1 <--previous primary
Note that it can take some time to make the domain changes so if you have live sites they could be down for up to 24 hours. I'm pretty sure you also won't be able to use some things Godaddy has like the "stats".