@flippnswitchez On a CoreXY swapping the motors reverses an axis. There are 8 combinations:
Motor 1
Motor 2
X Motor forward
Y Motor forward
X Motor forward
Y Motor backward
X Motor backward
Y Motor forward
X Motor backward
Y Motor backward
Y Motor forward
X Motor forward
Y Motor forward
X Motor backward
Y Motor backward
X Motor forward
Y Motor backward
X Motor backward
One of these combinations will always result in a left handed cartesian system. The other combinations will result in either a right handed cartesian system, reversed axises, or swapped axises. The exact setup you need depends on your motor location, wiring, and possibly belt routing.
For reference you ultimately want a left handed cartesian system. This is important because a right handed system will print things backwards, this isn't a problem 90% of time but is maddening 10% of the time. The correct cartesian co-ordinate system looks like this:
0_1523851005936_Cartesian System.png
Purple is the location of my end stops so they are configured for X min, Y max and in my homing files I tell the printer to "home" to back-left corner.