The Global Mapper workspace maintains the list of all currently loaded overlays as well as some state information about each of those overlays. When the workspace file is loaded, all of the overlays that were loaded at the time the workspace file was saved will be loaded into Global Mapper. This provides a handy way to easily load a group of overlays which you work with often.
The Global Mapper workspace will also contain any changes that you have made to loaded vector features as well as any new vector features that you have created. The user projection and last view on the data will also be maintained.