The positions on the neck comes from the notes used in a particular scale. Since each scale has different notes, each scales has different position. The key in finding positions is to know your fretboard and which notes are where.
A minor pentatonic
Notes : A - C - D - E - G
A major pentatonic
Notes : A - B - C# - E - F#
So to answer you question, the difference between A minor and A major is they use different notes and since they use different notes, they have different positions on the neck.
I'll take myself as an example. I'm a visual person. I remember patterns and position more than actual notes. So when I start playing over a backing track, I see where I need to play, but I couldn't tell you on the spot what are the notes in the scale I use. I'd have to stop and think about it.
In the beginning I learned scales and positions on the fretboard without knowing I was actually playing a specific sequence of notes. after years of playing I started asking question and that's when I learned that a scale is made up of a bunch of notes.
The best tutorial we have on learning the pentatonic (minor and major) scales is probably Christopher Schlegel's "Pentatonic Scales & Frameworks". What is great about his tutorial is that he will not only show you the pattern, but the logic behind it also.