There is a specific command for mapping input to a display in xsetwacom called MapToOutput. Here is what you do:
Start by figuring out the name of the display you want to map to. This can be done by running xrandr:
phnomic@phnomic-jobb:~$ xrandr
Screen 0: minimum 320 x 200, current 3200 x 1597, maximum 8192 x 8192
LVDS1 connected 1280x800+1920+797 (normal left inverted right x axis y axis) 286mm x 179mm
1280x800 60.0*+
1024x768 60.0
800x600 60.3 56.2
640x480 59.9
VGA1 connected 1920x1200+0+0 (normal left inverted right x axis y axis) 518mm x 324mm
1920x1200 59.9*+
1920x1080 60.0
1600x1200 60.0
1680x1050 60.0
1280x1024 60.0
1440x900 59.9
1280x960 60.0
1024x768 60.0
800x600 60.3
640x480 60.0
HDMI1 disconnected (normal left inverted right x axis y axis)
DP1 disconnected (normal left inverted right x axis y axis)
HDMI2 disconnected (normal left inverted right x axis y axis)
HDMI3 disconnected (normal left inverted right x axis y axis)
DP2 disconnected (normal left inverted right x axis y axis)
DP3 disconnected (normal left inverted right x axis y axis)
In my case I want to use LVDS1.
Next, figure out what your devices are called. This is done using xsetwacom --list:
phnomic@phnomic-jobb:~$ xsetwacom --list
Wacom ISDv4 E6 Pen stylus id: 20 type: STYLUS
Wacom ISDv4 E6 Pen eraser id: 21 type: ERASER
Wacom ISDv4 E6 Finger touch id: 22 type: TOUCH
Finally run the command xsetwacom set "[device name]" MapToOutput [screen name] for all devices that you wish to assign. In my case, this becomes:
phnomic@phnomic-jobb:~$ xsetwacom set "Wacom ISDv4 E6 Pen stylus" MapToOutput LVDS1
phnomic@phnomic-jobb:~$ xsetwacom set "Wacom ISDv4 E6 Pen eraser" MapToOutput LVDS1
phnomic@phnomic-jobb:~$ xsetwacom set "Wacom ISDv4 E6 Finger touch" MapToOutput LVDS1
And then you are all good to use your fancy touch screen regardless of what monitors you connect it to and what orientation you use for your monitors.
If you want to know more, I recommend this sourceforge post.
Best Answer
Have you tried using xinput-calibrator?