There are five categories of rune: Weapon, Armour, Talismanic, Standard and Engineering. Runes from each of these categories can be inscribed upon an item carried by certain models or units, thus creating a runic item. To do this, simply choose the runes you want a model or unit to have and note down their names and the item they have been inscribed upon when writing your muster list, remembering to add the cost of each rune to that of the model, just as you would for a magic item.
For example, you may wish to inscribe a Weapon rune upon the hand weapon carried by a Dwarf Thane, effectively arming that model with a magic weapon. After choosing from the list of Weapon runes, simply record on your muster list that this Thane wields a hand weapon inscribed with your chosen rune.