I probably don't have the same pad as you, and I use Krita, but xsetwacom will likely be the tool.
See what it calls your device
See everything it can set
Code:
xsetwacom -s --get "Wacom Intuos S Pad pad" all
This turns off the 1st button on mine
Code:
xsetwacom set "Wacom Intuos S Pad pad" "Button" "1" ""
Once you get the right functions set for the buttons, put the commands in your shell startup scripts so they stick at next reboot.