Okay I understand what a scale is and I have a good enough idea what a box is. But whenever I see them on a tab it confuses the hell out of me. Like for example in the song Bury Me in Smoke by Down, for the solo it says this:

B Pentatonic Minor

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Box 1:
|--1--|-----|-----|--2--| -1st string
|--4--|-----|-----|--5--|
|--2--|-----|--3--|-----|
|--5--|-----|--1--|-----|
|--3--|-----|--4--|-----|
|--1--|-----|-----|--2--| -6th string

10th fret

Box 2:

|-----|--2--|-----|--3--| -1st string
|-----|--5--|-----|--1--|
|--3--|-----|--4--|-----|
|--1--|-----|-----|--2--|
|--4--|-----|-----|--5--|
|-----|--2--|-----|--3--| -6th string

12th fret

So if its on the twelveth fret for the second one, does the 2 and 3 on the 6 strings mean 2 and 3 from there? Such as 14 and 15? If so, why the hell is it written like that? I mean I would think each column is a fret but then what are the numbers? Can someone explain this to me?
nope, the 1,2, and 3, etc. represent the degree of the scale that that note is...for example, on the first box there, the one means the first degree of the B pentatonic that is or the root note, or specifically the B note. the two means the 2nd degree, and so on. the pentatonic scale only has five notes, which is why the numbers only go up to five. hope that made sense
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Those numbers are just indicating which note in the scale that fret is.

All the root notes are marked 1, for example.
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The "boxes" are a way to demonstrate a basic scale shape on paper, but as you will find out later they are more guidelines then rules.

The basic "box" is something of this nature:

-------
-------
------5
--3-5--
3------

That outlines the important notes in any "key", which as you will find out later is just a scale that works over a chord.

The notes above will work above any G chord (except Gdim and some other funky ones). If it's Gm, there will be a 6 on the E string, if A Major, it will be a 7.

The notes you add to that box (which is the root, the fourth and the fifth of a chord) depend on the name of the chord - Major, minor, 7th, etc. - and what you want to do with it. Playing 2 on the A string will give you a major third, a nice sounding harmony. Playing 4 will give you a tritone, a dissonant or very tense-sounding anti-harmony.

Blue players use tritones, fifths and sevenths to create and resolve tension over various chords so their music simulates crying or having sex or beating your wife...blues stuff.

Jazz players "pop" in and out of different scales to create different moods or "modes" weaving together a unique melody that can include all 12 of the notes on the guitar (yep, only twelve!)

...and so on.

Boxes guide you until the "AHA!" moment where this all solidifies and becomes muscle memory. Until then, practice those boxes!

And good luck.
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I think I get it a little better now. Thanks guys.