When you use a spell with multiple instances of damage (e.g. Echo, Drown in Flames), do you consider the combined damage dealt or each damage instance when evaluating Well of Despair (When a player deals 6 or more damage to the nemesis with a single spell, add a power token to this card.)?
You consider the total damage dealt by the spell to the nemesis. When cast, a spell will add at most one power token to the card (note that Echo spells are cast once, evaluated twice).