This figure show me the difference between demo(cloned from GitHub) and demo2(created locally and initialized into a repository), the folder .git is hidden by default.
This tell me for a repository(created and initialized locally), using packages in Atom cannot push until now.
git-plus is just a more beautiful and easier shell of git than git-bash, so you have to set git path like the figure below, and it cannot clone from remote repository.
Conclusion: GitHub Desktop and git-bash is perfect solution for all git operation.