If you examine the Layout image you will see that the notes on the nut go E A D G B E from bottom to top. The E on the bottom being on the thick E string and the one on the top being the thin one.
This is what I refer to as the 1st Perspective in Fret Sage. I think of it as the way a person holding the guitar may perceive the fretboard.
The 2nd Perspective option however it the complete opposite With the top E being the thick string and the lower E being the smaller one.
This perspective is more akin to someone that is observing the fret board on a guitar that someone else is playing. Though still technically backwards.
