When are Skydrive or Microsoft Drive as it will probably be called going to allow you to choose what specific folders to sync.
This is the only reason I don't actually use SkyDrive as my default choice of cloud storage service.
My system setup is
My main internal hard drive for all the operating system & files
External hard drive for all of my own personal files
If SkyDrive let me choose what folders to sync then I could actually work in the cloud properly
So I could for example sync