The word "position" can mean two different things in relation to playing scales on the guitar.
Firstly, it can describe where you are in relation to the fretboard, regardless of key: if the first finger is at fret 1 you are in first position; if the first finger is at fret 5 you are in fifth position. A classical guitarist would usually use the word "position" in this way, it is common for other guitarists to as well.
Secondly, it can describe the different scale patterns produced by starting on the different notes of a scale (the correct term for the different notes of a scale is degrees). For instance, the scale of A minor pentatonic has these notes: A C D E G. If we play these notes starting from the root note, A, this could be described as the "first position" of this scale. Personally, I would refer to this as the first mode of this scale (although the "first mode of A minor pentatonic" is most easily described simply as "A minor pentatonic"!). If we start on the second note, C, this would give the notes C D E G A; this could be described as the "second position" of A minor pentatonic, but more accurately it is the second mode of A minor pentatonic. (It is also C major pentatonic, but that is a whole other thing...!)
The confusion between the two uses of the word "position" can be demonstrated quite easily. The first mode of A minor pentatonic starts on the root note, A. In the OP's terminology this is "Position 1 of A minor pentatonic". But, as it starts on fret 5 (if you start on string 6) many guitarists would say this is in fifth position!
So, confusion can be avoided in a couple of ways: either by using the word "position" solely to refer to the position along the neck (i.e. which fret finger 1 is at) and using the word "pattern", "shape" or "mode" to refer to the various scale patterns created by starting on different scale degrees; or, by being very clear about the use of the word "position", for instance, saying that Position 1 of A minor pentatonic is in Fifth Position.
Whichever terminology you use, it is a really good idea to learn how to play the notes from each scale in a number of different positions along the neck. This means that you are not restricted to simply a couple of octaves of that scale, but can play a greater range by moving to another "position" of the same scale. Learning to play the notes of a scale with different patterns produced by using different starting notes will also help you to learn all the modes of any particular scale (although it is important to point out that these are not always the same thing! The basic reason for this, is that playing a mode strictly you would usually practise playing between the same pitches, eg. A-A or C-C; when practising the different "positions" or patterns of a scale you often include all the possible notes within the range of your fretting hand in that "fret position").
Initially it makes sense to learn the notes of a scale starting on the root note. It is certainly my experience that most guitarists do this. This would be mode 1 of the scale and would be what the OP calls "Position 1". A common pattern for playing a minor pentatonic scale starting on the root note is shown below:
In order to play this in any key you would move this pattern up and down the neck (the other meaning of changing "position"!) Below is a list of pitches on String 6; this tells you which fret to start on to play a minor pentatonic in any of the twelve keys, using the pattern above:
- Open: E
- Fret 1: F
- Fret 2: F# or Gb
- Fret 3: G
- Fret 4: G# or Ab
- Fret 5: A
- Fret 6: A# or Bb
- Fret 7: B
- Fret 8: C
- Fret 9: C# or Db
- Fret 10: D
- Fret 11: D# or Eb
- Fret 12: E again (the octave point, halfway along the string, the double-dot)
In order to learn the different patterns of the pentatonic minor you would start on the different degrees of the scale, and play all notes (or exactly two octaves if playing as a mode) of this scale reachable within that position. So, the patterns/modes of A minor pentatonic would be ordered like so:
- Mode 1 (which we would just call A minor pentatonic): A C D E G
- Mode 2: C D E G A
- Mode 3: D E G A C
- Mode 4: E G A C D
- Mode 5: G A C D E
If I get a chance I'll do a diagram for all of these, but the OP links to this web page which shows these patterns.
Many thanks to CalebHines and Scott (the OP) for their comments which really helped me rewrite this answer - I can't believe Scott accepted the answer initially...!