Ok in a nutshell;
- You can stack your +1 headpiece attribute, for example on your Ele it could be +1 Fire Magic) with ONE other Fire Rune (from Minor to Superior) giving you a chance to get ONE off your attributes a nice comfortable +4 bonus.
- You can only achieve a maximum boost of +3 to any OTHER area than your head piece (from one superior rune)
- The exception runes are the runes that boost your HP or Energy by SMALL amounts. I think they are Vitae and Attunement? +2 Energy or +10hp. These can stack (up to a maximum of 5 - 1 per armor piece)
Insignia, Im not too sure how to explain.
Some special insignia, for example the Necromancer "Bloodstained Insignia" can be applied to only ONE piece of armor, as any more WILL NOT STACK. However, if you have an Insignia that offers extra armor vs, for example, Elemental damage, it might be advisable to put them on ALL your armor.
The same is true with the +energy Insignia, Radiant. This can (and perhaps should, with some exceptions) be applied to ALL your armor for the maximum benefit.
If you need to learn more, create a PvP character and , once in game, press your J key. You can play with various armor and Insignia here, and see how it effects your attributes, energy, hp etc.
Hope this post helps.
Edit: As to your elementalist, I am not sure why the rune won't apply. Be sure you are applying it to armor, and that it has been salvaged from its armor (if you found it). Also, check you don't already have one, and remember you must ACCEPT the little dialogue window that asks you if you are sure you want to make the changes to your armor