The SCM is very much improved, but I swear there is still a bug (that I have seen since the WWDC beta, and reported) with it which annoys me.
You can pretty much do all your management of branches and the repository itself from XCode, which is much nicer, but adding folders to, or moving folders to the root of a repository is bugged. It just didn't work the last time I tried. If you want to do that, you need to drop back to the CLI. To get around it, I would just create a root node for the project via the CLI, and then use XCode to manage the project once that node was created.