One thing you might want to keep in the back of your head...
I've run into problems with LONG filenames...not the regular 'longer than 8.3 filenames' but the kind of filenames that include long path and make the entire 'path/file' name over so many characters (i.e. when storing your programs in MyDocuments).
I tend to keep everything in the root directory these days (PBP, MCS, program storage, include files, and so on). Never had a problem with it, don't have to worry about it.