In Maya by default in project setup lots of different folders. So each time you start a new project you have to rewrite or delete most of them. To save your time you can just change default project folders.
To do this find \Maya\scripts\others\np_getFileRuleWidgets.mel (in Maya 2012 this options splited on two files: Primary Project Location - np_getPrimaryProjectFileRules.mel and Secondary Project Location - np_getSecondaryProjectFileRules.mel), and just edit this scripts as you want.
To do this find \Maya\scripts\others\np_getFileRuleWidgets.mel (in Maya 2012 this options splited on two files: Primary Project Location - np_getPrimaryProjectFileRules.mel and Secondary Project Location - np_getSecondaryProjectFileRules.mel), and just edit this scripts as you want.