If my walls extend about five inches past my Schach support beams is that an issue? Does the Schach need to "top" the sukka or can it rest a few inches below the top of the walls?
In the mishnah it says that if you have a sukkah on top of a sukkah, if you can't use the upper one, the lower one is kosher. I would assume in that case the walls extend above the schach.
The walls may be higher than the schahch. It is kosher. It would seem that such a thing violates none of the laws of building a kosher Sukkah. Another proof to this (besides what Shmuly wrote about a Sukkah above a Sukkah) is that all walls which are at least 10 handbreadths tall (this is the halachic definition of a wall from a halachah l'Moshe mi'Sinai) are viewed as if they extend above into heaven (and certainly past the schach, if the wall is at the edge of the schach). This law is called "Gud Asik" (extend it above). For more detail, see Gemara Sukkah 4b.