As the first person installing the x-kernel at your site, you should look over the makefiles in /usr/xkernel/build/Template. They have many site-specific parameters referring to compilers, libraries and the like which should be set to reflect the environment at your site.
The x-kernel is distributed with two versions of the protocol number table in /usr/xkernel/etc, prottbl.std and prottbl.nonstd. Since several example graph.comp and rom files refer to a file named prottbl in that directory, you should probably copy or link the version most appropriate for your site to this name. See section 13.1 for a description of the difference between the two.