With creation of a new repository, there is no master branch.
With Egit you can't clone an empty repository:
//"Source Git Repository is empty"//
Therefore you have to install mssysgit; init a local repo and push it to your repo created via scm-manager.
If scm-manager could create a master branch, it would be possible to create the local repo within eclipse and push it directly to scm-manager.
No more need (almost) for a native git client.