To unlock the element runes, you will first have to reach level 50 and do'Main' quest. Doing so will unlock the Element function where you can obtain runes. Then you'll be able to place the runes in the Mount Window, up to four runes at the same time.
If you want to change or insert a rune, simply click on the rune spot and choose the rune you would like to apply to that slot. You can also unequip a rune completely by pressing 'unequip', you may need to do this if you are trying to synthesis your runes to a higher level.
There are three  different types of runes: Flame, Thunder, and Hail, and they will either be ATK, or DEF. The maximum level you can synth runes to is Lvl. 10. You are able to synth runes through two different ways.
-By using the 'Synth' window at the bottom of your screen. In this function, you can specify how many you would like to synth.Simply choose the one you can and want to upgrade. For example to make 1X lvl 7 rune u will need to have 5X of lvl 6 runes. like it is show in the picture below.
-Opening your inventory directly and choosing the rune you would like to synth, and pressing 'Synth'. Doing so this way, it will synth as many as the system can, meaning if you have 10 and press 'Synth' it will synth 2, as you can't specify a quantity doing it this way.
As of now, there is a total of 101 stages in Element, with a max of 303 stars. (The last chest at the moment is 300). By reaching higher stages, you can obtain higher level runes and rewards. You will be able to open the chest every 15 stars. You should always Blitz the last stage if possible for the best rune rewards.
Lvl 40-Lvl 54 = Level 1 (1st-4th Stage) & 2 (5th stage)
Lvl 55-Lvl 69 = Level 2 & 3
Lvl 70-Lvl 84 = Level 3 & 4
Lvl 85-Lvl 99 = Level 4 & 5
Lvl 100+ = Level 5 & 6
Element works the same as Tartarus, you'll be unable to Blitz a stage until it's 3-star.
How the do Element
1. Press the 'Challenge' icon
2. Choose 'Element'
3. Check the elemental monster you are going to attempt to fight. By equipping the element they are afraid of, you will be able to defeat them easier.
4. Press 'Challenge' to begin the fight
*Use the goddess Nemesis for your elemental challenges, as she will help you kill the monster quicker.
*Choose the runes the monsters are afraid of (as shown in step 3)
*If you're having trouble and getting hit too hard by the monster, try equipping the DEF rune of the element you are attempting as it can dramatically lower the damage taken, meaning less potions for you!
ELEMENT POWER IN PVP.
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* You can also gain some Element status from MOUNT TRANSFORMS as well! Each Mount you unlock has a special bonus, and it will increase with every upgrade you do that mount (0 star > 1 star, etc)