Managing projects

I'm trying to ensure that all of the files associated with a project or stored in that project home directory including the xml files and the hzp .etc. How can I do this?  I have multiple projects that requirement flash placement and memory map modifications. I keep writing over previous files becomes the import places them in the $ProjectDir instead of the home directory of the actual project folder. For example, I would like to have Crossworks Projects as the root folder and store all of my individual projects under it.  Can this be done?