On my machine, there is:
/usr/X11R6/include/X11/Xaw{,3d}
... and /usr/include/X11 -> ../X11R6/include/X11/
I've found that it is important that /usr/X11R6/lib is BEFORE
/usr/X11R6/lib/Xaw3d in /etc/ld.so.conf, otherwise, XEmacs is built
with flat athena headers, but run-time links to athena3d.
Hope this helps.