where do the +1 come from in 12 +1 +1?

Just looking at this build, http://pvx.wikia.com/wiki/Build:W/an..._Slash_Warrior

strength = 12 + 1
swordsmanship = 12 + 1 + 1

do all those +1 bonuses come from the helmet bonus, and 2 minor rune bonuses?

Yes they are the inherent headpiece bonus and a minor rune.

12 + 1 is a minor rune on armour pieces............12+1+1 is a minor rune on a headpiece...headpieces have an auto +1 to there attributed rune

What they said

You can replace Fire Magic with each other attribute;

Attribute level = 12 Fire Magic
Headpiece = +1 Automatic.
Rune = +1 (or 2 or 3).
Total =____14 Fire Magic.

Impossible to get 5x +3 Fire Magic by the way. It is possible to put it on your armour, but it wont count.

Health and energy insignia's stack. So for every one of them implemented in your armor, you get the bonus. Runes of some sort of mastery don't stack. Neither to runes of vigor. Runes of Vitae and Attunement do stack. I'm sure there is a list of things that stack and don't stack on wiki.

What would be the best rune combination on an assassin armor? I guess a superior health rune, and how would you divide the other insignias/runes?

Almost always:
12 + 1 + 1 Dagger Mastery
12 + 1 Critical Strikes
Superior Vigor
optional (vitae usually)
optional (vitae usually)

For insignias I use blessed on my assassin, because he always has Strength of Honor from a smite hero and Critical Agility.

I say go with major rune 12 +1 +2 0n the helm for 15attribute on any char, whats you take on that, its only a -35HP penalty not like earlier when it was -50HP, your not giving up much for the extra damage

I would also carry spare armour pieces for other builds, this is common across all character classes.

High energy armour, farming armour etc
Several headpieces with +1+1 dagger mastery +1+1 Shadow etc