I recently sorted this out, so I thought I'd share the scripts that worked for me on Saucy Salamander Ubuntu 13.10 with Unity.
First, work out which device you actually want:
$ xsetwacom --list
Wacom Bamboo stylus id: 11 type: STYLUS
Wacom ISDv4 E6 Pen stylus id: 13 type: STYLUS
Wacom ISDv4 E6 Finger touch id: 14 type: TOUCH
Wacom Bamboo eraser id: 19 type: ERASER
Wacom Bamboo cursor id: 20 type: CURSOR
Wacom Bamboo pad id: 21 type: PAD
Wacom ISDv4 E6 Pen eraser id: 22 type: ERASER
xsetwacom to get the right touch input relating to the correct screen, even with multiple monitors:
$ xsetwacom set "Wacom ISDv4 E6 Finger touch" MapToOutput LVDS1
At this point I should point out that my touch screen is incorrectly configured and therefore needs the script above running every time I plug or unplug an external display. Since I dock my machine, move it almost daily, and regularly present ... that's kinda irritating. Any solutions on improving that are welcome.