The method should be:

1) Set the pin active low setting according to driver requirements in the pin setup
2) Adjust the axis direction using the reversed checkbox in the homing setup.
3) Now that the axis move in the right direction, deppending on where you have the home switches, set the home negative checkbox for each axis

Now you should have the axis direction properly configured

Regards

Both of you are patient! It works now with the x-axis in reverse and then the neg direction unchecked. That seems to fix it without messing with the gcodes.

Thanks  for the help guys, I appreciate it!