I'm not sure about enforcing main.pde (or anything else for that matter). You should be able to define the file name and location anywhere you like and the working files (.HEX etc) should also go to the same position or a folder under that.
Also to have to search around users/me/roaming/??????? is crazy, and as I understand it they all get deleted when you close the IDE, presumably because otherwise you'd wind up with a 1000 temp folders.
So don't have the temp folders in the first place.