When you first start Eclipse, the IDE prompts you to choose a workspace directory.
A workspace can be thought of as a logical grouping of projects, settings, preferences and metadata. Much like a real desk, a workspace is a place where work is done though that does not infer any relationship between the things on the desk.
Having multiple projects in a workspace does not imply any relationship between the projects. Neither do projects have to be located under the workspace directory, although you can choose to do that.
A workspace can only be used by one instance of Eclipse at any one time but it is perfectly reasonable to run multiple instances of Eclipse each using a separate workspace.
When running multiple instances of Eclipse, you can change the title of each Eclipse window, which gives you an easy way to identify which Eclipse is using which workspace. To do this, click Window > Preferences, then click the General > Workspace tabs in the Preferences dialog box, and specify a name in the Workspace name (shown in window title) field.
To change the workspace the current instance of Eclipse is using, click File > Switch Workspace and either select one of the available workspaces from the menu, or click > Other and specify the path to a different folder you want to use.
Generally, we do not recommend that you commit workspaces into a source control system, as they contain metadata which is updated frequently.