We recommend you to store several projects per repository, simply in order not to have too many repositories to deal with. However you can choose to store only one project per Git or SVN repository, if you prefer so.
For more information on how to configure your version control systems, see Setting up your version control system.
You can also have several version control repositories each containing several projects. For more information on how to create projects and store them in Git or SVN, see the Talend Administration Center User Guide.