#1 Is there a way to change which monitor is 0,0 ?
I think so. In your case, I think the following command could change HDMI1 to position (0,0)
xrandr --output HDMI1 --pos 0x0 --output VGA1 --right-of VGA1 --auto
#2 Is it possible to set the x axis as a negative number?
I tried lots of linux distributions from both CLI/GUI but never successfully changed x/y axis as a negative number, please tell me if you find one 