This is the directory structure you will end up with following the instructions in the Installation Guide.
|-- home
| |-- git
| |-- .ssh
| |-- gitlab
| |-- gitlab-satellites
| |-- gitlab-shell
| |-- repositories
/home/git/.ssh
/home/git/gitlab This is where GitLab lives.
/home/git/gitlab-satellites Contains a copy of all repositories with a working tree. It's used for merge requests, editing files, etc.
/home/git/repositories Holds all your repositories in bare format. This is the place Git uses when you pull/push to your projects.
You can change them in your config/gitlab.yml file.