Well the project has to define some folder lookup structures, and the base folder path needs to be defined as well. And every time you open a scene you must ensure that you've set the project right for THAT scene (maya will just keep the project folder when if you open a different project scene, the guess what project you were in if you failed to tell correct structure then maya might just guess wrong)
Read mayas manual they have a chapter on this. It will actually save you time to understand how maya works you know. (likewise ha you read the entires in the manual youd also had known about dirmap)