From the terminal (or command line prompt in Windows) goto the non empty directory where you'd like to create a Git Repository
Run the following commands
git init
git add .
git commit -m 'Initialized my Git Repo'
Get the url of your remote repository.
For E.g in case the url is https://xyz@bitbucket.org/xyz/sample_repo.git
Run the following commands
git remote add origin https://xyz@bitbucket.org/xyz/sample_repo.git
git push -u origin master