If your X, Y and Z axis are not oriented correctly, you may need to fix this.
Step 1: Inside the setup window select the setup tab (the first tab).
Select the 'Model Orientation' drop down menu.
Select the 'Select Z Axis/Plane & Y Axis' option.
You will notice that the Z Axis cursor icon is now select prompting you to select the Z Axis...
Step 2: To select the new axis:
Select the Z axis cursor.
Select the Z axis as shown.
Select the Y axis icon.
Select the Y axis as shown.
You may also need to select the radial button to 'Flip Z Axis'
Select the 'Box Point' cursor icon and select the corner shown - The corner should be the bottom left corner on the top face.
Please note that when you complete this stage successfully the Z axis should be pointing up towards the sky...