The location of runes doesn't change their effectiveness. But since warriors switch helmets (and sometimes gauntlets) when they switch weapons, most people put their weapon runes on their helmets.
Since I often use my PvE characters for PvP and I always buy 15k armor I put the superior runes on the head. So I buy 15k armor on different body parts exept on the head where I put a 1.5k armor. Than I buy multiple 1.5k armors for head (helmet) and put superior hammer, axe and sword on it and switch between them depending on the build. If a helmet is realy cool than I buy 1 for 15k but the rest for 1.5k and "hide" (dont show) the helmet when I use them.
Here's how I've got my Warrior set up:
Superior Axe mastery on Executioner's helm (cheapest armor piece and can be switched for sword or hammer helm)
Superior Vigor on chest - Most Expensive armor piece, with the vigor rune on it, you don't need a second one.
Sup. Absorbtion on leggings - 2nd most expensive armor piece, again with this rune, you never have to change.
Minor tactics on gauntlets
Minor Strength on boots - these last two really don't matter which way you go.
Make sure to put your Superior Vigor on a piece of armor that you won't want to change. Trying to salvage it usually leads to the destruction of the armor piece.