Currently I have made a slight modification to /usr/share/Eterm/themes/Eterm/theme.cfg and menu.cfg. My custom configs get erased every time I do an upgrade through dselect. This should work like all other debian packages do when they detect a changed configuration file, prompting the user for a diff or overwrite or keep existing copy or whatever.
I suggest using dpkg-divert on any package-space files you modify beyond /etc files -- which are automatically handled as conffiles.