Here's the deal with scales, you can play a scale from any fret, it's moveable. BUT if you want to move up and down the guitar neck without changeing key, you have to play a different form of the scale. 1st position is the first in a minor scale. 2nd is the first in a major scale. So if you play first position from the first fret, then the scale is in Fminor, but if you play 2nd position from first fret, then you are playing in F major. I have put the scales in F minor. I hope that made sense, even though it probably didn't.

1st position

e-------------------------------1-4-4-1------------------------------
b-------------------------1-4------------4-1-------------------------
g-------------------1-3-----------------------3-1--------------------
d-------------1-3----------------------------------3-1---------------
a-------1-3---------------------------------------------3-1----------
e-1-4--------------------------------------------------------4-1-----

2nd position

e-------------------------------4-6-6-4------------------------------
b-------------------------4-6------------6-4-------------------------
g-------------------3-5-----------------------5-3--------------------
d-------------3-6-----------------------------------6-3--------------
a-------3-6---------------------------------------------6-3----------
e-4-6--------------------------------------------------------6-4-----

3rd position

e-------------------------------6-8-8-6------------------------------
b-------------------------6-9------------9-6-------------------------
g-------------------5-8-----------------------8-5--------------------
d-------------6-8----------------------------------8-6---------------
a-------6-8---------------------------------------------8-6----------
e-6-8--------------------------------------------------------8-6-----

4th position

e------------------------------------8-11-11-8-------------------------------------
b-----------------------------9-11---------------11-9------------------------------
g----------------------8-10-----------------------------10-8-----------------------
d---------------8-10-------------------------------------------10-8----------------
a--------8-11---------------------------------------------------------11-8---------
e-8-11-----------------------------------------------------------------------11-8--

5th position

e--------------------------------------------11-13-13-11------------------------------------------
b-----------------------------------11-13------------------13-11----------------------------------
g--------------------------10-13-----------------------------------13-10--------------------------
d-----------------10-13----------------------------------------------------13-10------------------
a---------11-13--------------------------------------------------------------------13-11----------
e-11-13------------------------------------------------------------------------------------13-11--

And back to 1st position, but this time play it from the 13th fret

e---------------------------------------------13-15-15-13-------------------------------------------------
b-------------------------------------13-15------------------15-13----------------------------------------
g----------------------------13-14-----------------------------------14-13--------------------------------
d-------------------13-14-----------------------------------------------------14-13-----------------------
a----------13-14-----------------------------------------------------------------------14-13--------------
e-13-15-----------------------------------------------------------------------------------------15-13-----

And so on and so forth.

You can play these scales over a song in the same key and it should sound good. Unless there's some wierd chord, but i don't feel like explaining that right now. And btw, there's probably gonna be a wierd chord.