If you look at your armor the the name is formatted like this
Insignia Name Name of the armor Name Of The Rune

You can have 5 runes and 5 Insignias
BUT they have to be a different type
The only runes you can stack are:

Rune of Attunement Energy +2
Rune of Vitae Health +10

To start with runes you might want to go with
Rune of Attunement and Vitae Health with a 1/3 ratio.
If your a caster go with 3 Attunement.
If your a melee go with 3 Vitae Health.

Your head gear is a special case.
ONLY Profession-specific runes should be used on your head gear.
The will let you change you head gear to fit your build.
For exampled a warrior might have 3 different helments

a helmet with +1 Axe
a helmet with +1 sword
a helmet with +1 hammer

And you can ALWAYS put a better rune over the top (replace) of your old runes.