Crystals recipes are the blueprints you will want to follow here. You can either read those recipes in your in-game Codex, under the Magic & Religion section, on the online codex, or simply in the crafting interface itself. However, since that interface is not available far from the Autel at Camp / Vigil, you may have to use the other sources at some point.
During this guide, we will follow the Glowing Stamina Crystal recipe.

Once you have all the reagents at the ready, creating a crystal via the new Enchantment interface is as straightfoward as creating a potion. You'll however need to be close to the Autel, otherwise the scripts will let you know it's a deal breaker.
So, keep close to that Autel and simply use your Enchantment skill.

See ? I told you the interface wouldn't be troublesome. The scrolls you found and learned are sorted accordingly to their rank and type. Since we're looking for Glowing Stamina Crystal select the second rank and browse through the list until you reach the Crystals section and that specific recipe.
Should you need more than one crystal, you could simply craft several crystals in one go by using the available quantity field :
Because of how the scaleform interface handles things, you may need to leave your mouse cursor over that quantity field in order be able to change its value.
Once you're all set, simply create your items via the - duh - Create Item button.

That's it. Shazam etc, your new crystal is immediately available in your inventory.
Speaking of inventory, please note that the Enchantment interface only checks your party inventory for the required reagents. If the reagents are - say - in your enchantment storage chest, the interface won't be able to find them. Because of how the interface connects to the scripting part of the game (long story short : those two parts can't interact !) there is nothing to do about it.

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