Though this post is ancient I figured I'd answer it anyway as I discovered upon trying to solve the same problem (four years later, lol).
The old way would be to put the following in your /etc/X11/xorg.conf.
Code:
Option "ClickFinger2" "3"
The new way would be to create a HAL policy file /etc/hal/fdi/policy/11-x11-synaptics.fdi.
Code:
<?xml version="1.0" encoding="ISO-8859-1"?>
<deviceinfo version="0.2">
<device>
<match key="info.capabilities" contains="input.touchpad">
<merge key="input.x11_driver" type="string">synaptics</merge>
<!-- Arbitrary options can be passed to the driver using
the input.x11_options property since xorg-server-1.5. -->
<!-- EXAMPLE:
<merge key="input.x11_options.LeftEdge" type="string">120</merge>
-->
<merge key="input.x11_options.ClickFinger1" type="string">1</merge>
<merge key="input.x11_options.ClickFinger2" type="string">3</merge>
<merge key="input.x11_options.ClickFinger3" type="string">2</merge>
</match>
</device>
</deviceinfo>
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