CNC3D Commander Users

Hi people, I am new to cnc 3d and cnc in general. I do however have previous experience with 3d printing and arduino. I am running the 3018 cnc pro. I have added limit switches to my machine. Max and min. My issue is, when I have the machine run through the homing cycle, It goes to home. Z is all the way up, X to the left, and Y (the tray) all the way toward the back. On the cnc it says x = -331 , y = -2, and z= -2. Is there a way to update it? or have I set it wrong?

I also try to engrave a design, It sits about 15mm above the actual block of wood (6mm).