Using essence to improve the land is no longer in the game.  You used to have to permanently expend essence to prepare the land before building each of your cities.  If the manual discusses it, it must have been written before the current release.

Essence now controls your maximum amount of mana you can have.  You expend mana by casting spells, but it re-accrues at 1 mana point per turn up to your current essence level.

If you research the "Imbue Champion" spell you can also transfer your essence to some of your units, which will allow them to cast spells, but if you do this your sovereign won't have as high an essence level as he did before.