Special Awakening, also known as combining Runes is very simple. It works very similar to how regular combining works. Although instead of Gold, you pay with a small amount of 
.
To special awaken a rune slot, you must first awaken your monster.
 |
Once you awaken a monster a Special Awaken option will appear. |
|---|---|
 |
The Special Awaken system will randomly increase the current base % of the equipped rune up to 50%. Special Awakening will cost runes and jewels. The amount of runes and jewels needed depends on the base % of the equipped rune. The higher the base %, the more runes and jewels are needed. |
 |
And there you have it, you have successfully Special Awakened the rune. You can do this again until you reach 50% provided you have the amount of runes and jewels needed. |
Below is a helpful video that explains what Special Awakening is and how to use it.
Rune combo-0
Special Awakening