At player level 19 the feature Runes is unlocked. Here you can equip, unequip and upgrade runes at will to both your character and all your heroes. The rarity and category of the rune determine how high the attributes are per level.
Rune Category
Besides the different quality color runes there are 3 different categories per type of runes: Liberty, Order and Chaos. Liberty runes are runes without a special background color. Order runes have a white background and Chaos runes have a black background. It is not possible to have 2 identical category runes of the same attribute equipped on a single hero. It is possible to equip all 3 different category runes of the same attribute if you have to Rune Slots for them. The quality color of the rune does not allow multiple runes of the same attribute and category either.
Rune Slots
To unlock rune slots for the player you will need to earn Arcane Crystals that can be won at the Trial Abyss. By defeating certain stages of this trial a single Arcane Crystal can be won. To unlock rune slots for heroes you need to improve their Upgrade level. Every rune slot has a colored border around it. The color of the border determines which category runes can be equipped. Liberty runes can be equipped in any slot. Order runes can only be equipped in slots with a white border. Chaos runes can only be equipped in slots with a black border.
Resonance
Rune Resonance is a bonus given when you combine certain runes of certain levels. To find all possible Resonances combinations click the Resonances button at the top left of the rune equip window. When you equip the runes of the right category and minimum quality as shown in the Resonances window you are eligible to unlock the Resonance bonus. To unlock the bonus all runes need to be a certain level which can be seen when you hover over the icon of the Resonance. The 8-Rune Resonance is only available when you own a special rune for the player class or UR quality hero you want to use this for. Each has their own rune so make sure you choose the right one when you get this from events.
Pray
To earn runes you need to pray. Press the Runes/Pray button found at the bottom right of this window. When you are at the Rune Altar you have several choices to pray for runes. Praying costs gold. Pray buys you 1 random rune, Pray x10 buys a batch of 10 random runes. Blessed Prayer costs Prayer Notes. Blessed Prayer gives you for no additional gold cost either an orange or a red quality rune. Red runes can also be purchased by clicking the Rune Shop button or find the shop at the Trading Post. Auto Retrieve is unlocked when a player reaches VIP. You can choose an amount of gold you want to spend at once and auto recycle any unwanted runes of a certain quality.
At the right side you can find the runes that you currently have in your inventory. You can Quick Recycle them based on rarity which can be changed through a drop down menu. You can also sort all your runes based on their level and rarity. To avoid recycling runes you can click the Lock button and then click on the rune you want to protect. A locked rune will show a lock icon on the rune icon.
This guide is sourced from yabusame.