origin

Good evening I made a CNC plasma with a 6442 G rough controller. The machine works perfectly but when I ask it to run the home button it goes in the opposite direction to where I want it to. Even if i change origin of the drawing sheet, the machine continue to reset the axis (both x and y) in the opposite direction (with inversion command) .  i tried to change the "reverse" function but in this case the arrow on the ruida works opposite to manually move the machine. And the limit switch doesn t work. So i changed the polarity without direction inversion, and i changed the limit switch polarity. It seems working good but whe i switch on the machine the axis run very slow for a while then stop without error signal and everything die. The machine doesnt work any more. 
any idea ? 
im thinking to invert the cable on the motor....
thany you 
Cristiano