So. Many. Knobs.
There are several ways to configure synaptics, and as jggimi, on systems that support syntaptics the X server now automatically loads the synaptics driver.
Without an xorg.conf, you can use
synclient(1) or
xinput(1) to set your preferences, if you still prefer xorg.conf you'll likely have to prevent the autoconfiguration of input devices. I believe there is a reference to this on the mailing lists or in the -current FAQ.