if i understand your question, you would usually use the first position of the pentatonic scale when starting on the root note of the key you are playing in, and by first position i mean this patter, in the key of A minor:
---5---8---
---5---8---
---5---7---
---5---7---
---5---7---
---5---8---
the other positions would coorespond to where you were playing on the neck in relation to your root note, so if you were playing around the 8th fret, (the C major relative to A minor), you'd probably base around this shape:
---8---10---
---8---10---
---7---9---
---7---10---
---7---10---
---8---10---
and if you take all the shapes up to the octave:
---5---8--- ---8---10--- ---10---12--- ---12---15--- ---15---17---
---5---8--- ---8---10--- ---10---13--- ---13---15--- ---15---17---
---5---7--- ---7---9--- ---9---12--- ---12---14--- ---14---17---
---5---7--- ---7---10--- ---10---12--- ---12---14--- ---14---17---
---5---7--- ---7---10--- ---10---12--- ---12---15--- ---15---17--- (then to position 1 at the 17th fret for the
---5---8--- ---8---10--- ---10---12--- ---12---15--- ---15---17--- octave)
like dave said, these are just notes, just pieces of the puzzle. and it's just the same 5 notes over and over, so it's not rocket science. but it IS VERY important to master the fretboard, to be able to play no matter where you are on the neck, and to learn to seamlessly connect the notes you are playing up and down the fretboard, in very position. there's nothing worse than seeing someone who gets lost everytime they venture outside the 1st position pentatonic box.