You can swap motor outputs in Vehicle tab and test every motor position using the Output tab.
Number is motor output number.
NW (NorthWest),
NE,
SE and
SW are motor position in frame and name is displayed in Output tab, like
VTOLMotorNW.
If your wiring matches the Multiwii scheme the outputs will be in this order: 4, 2, 1, 3.