Different desktops use different methods. Unfortunately, it depends wholly on where the touchpad driver looks in your session. For example, Puppy Linux with JWM uses flsynclient, KDE uses (what at least used to be) Synaptiks. Really, it depends on which desktop you use. Generally speaking, it is best to leave it to whatever environment you use. If you use something like KDE and GNOME side-by-side, you may need to modify the X11 config files directly, because their individual settings don't interact. However, if you use GNOME or Xfce etc. almost exclusively, use the settings from that desktop.
The reason is simply convenience. If you edit X's configuration or use a third-party tool, when GNOME tries to shut off the touchpad, say for typing, it may be overridden by the environment. Extensions that manage touchpad will probably not work. Even if they do work, their settings are likely to be unreliable because when they do some automatic change, they will take over. On next reboot the system will have control because that's the way you have it set up.
The only case where another client is necessary is if you really need more settings than the environment you use offers.
Note that LightDM has its own user, and so you can log in using Su to change the settings. I believe that the lightdm user has a gnome control center as well and can set settings for touchpad that way, but I have no way of telling for sure.
Best Answer
Found it:
http://www.x.org/archive/X11R7.5/doc/man/man4/synaptics.4.html
Thanks to @Rinzwind for the link to synclient man page.