Before you can run a program, you must load it into a workspace. Workspaces enable you to create groups in which all query modules are related in some way.
The grouping is up to you. For example, groups can be created based on projects, or on individual developers, or on criteria you choose.
If more than one person loads the same query module into Studio, makes changes and then saves it, the last person to save will overwrite any changes that other people made. Using separate workspaces does NOT prevent this problem. Workspaces provide separation within the server, but not within the file system. Use a source code control system to avoid conflicting changes to a query module.