Hmm, this sounds like it might be the way you are approaching the IDE, or the way it is setup.
Specifically, the Arduino IDE requires the folder name for your project to be the same as the sketch file's name. For example, if I am making a sketch called
AlligatorCrossing.ino, this file should be in a directory also named
See this StackOverflow link on the subject. I have been meaning to write a guide so one does not need the IDE, but have not had a chance.
In order too bootstrap you, I might recommend the Codebender method for uploading games. Once you are confident that everything works with the unit. Then switch to the IDE.