debian/rules cannot patch itself, nor can debian/patches be used to patch debian/control or debian/changelog so emdebian patch files are located and maintained in the directory above the ${top_srcdir} of the package - where the .deb and .diff.gz files are created. The patches are then applied by emdebian-tools when a Debian package is "emdebianised", before dpkg-buildpackage or debian/rules are executed.