Enabling the Custom Desktops for users is easy. Simply create a symbolic link in /opt/thinlinc/etc/xstartup.d:
# ln -s /opt/thinlinc/bin/tl-desktop-activate.sh /opt/thinlinc/etc/xstartup.d/35-tl-desktop-activate.sh
The ThinLinc session startup will read this file and make sure the environment variable KDEDIRS is set correctly. It will also write a ~/.config/menu/applications.menu and possibly create symbolic links under ~/.kde/share/apps/kdesktop/Desktop. Your profile should then execute the command startkde.
The TLDC activation script only runs TLDC for non-root users. Test your TLDC configuration using a normal user.