By default, WebWorks Publisher Standard Edition maintains its relative directory structure if a project is moved. To change this setting, deselect the Keep these directories relative to the project if it moves check box. This means that the Output, Images, Support, and Temp directories would not move if you move the project file. By keeping directory relativity intact, you let WebWorks Publisher Standard Edition easily locate all of the files it needs. When Publisher cannot find the files, you will be prompted to supply the file locations when the project is opened.
If you need to move your projects to other computers or file systems, then you should keep this setting selected.