I am not sure if I will be phrasing this question in a form that makes any sense at all but here goes.
My motors are all running in the positive direction towards the ref/home switches. In the manual it says that it is normal for y and x to move in the negative direction towards the switch. When I try and run a g-code it seems to want to cut in the negative plane and so doing hits the limits. What am I overlooking . pls HELP!

Where do you set z=0? I use the top of the stock, and therefore all cuts will be in the negative direction, z home is set at the top of the z axis, but is only used as a means of getting the z out of the way, rather than a set datum point since I am using cheap micro switches. Hope this helps!

Yes, thanks that helped. but only after I tried to do that and it did not work. I eventually after an entire day of fiddling figured out that my calculations for steps per unit( which in my "wisdom" I had converted to metric while using an imperial screw) were horribly wrong! How I managed to mess that up soooo much boggles the mind. Also a tiny tick mark in the motor reversal box got everything running the right way and in the correct size. (chair)