You don't need to use (take out) the essences from the Inventory. The Inventory only lists them.

You use your essences right from your Collections. Open your collections and see there's a box with essence against each collection that shows the number required to complete a collection.

Simply tap the Assemble button against the collection that has enough essence and all items found. The essence will be used and recalculated automatically in your Inventory and against other collections that require this type of essence.