They are just 2 separate inputs in case the player has a character with levels in different caster classes which require being treated differently. Maybe cleric/magic user or some such. If the character has only caster levels in one class, they can be set equal to each other (can put @{casterlevel} in the casterlevel2 spot) or just use one and disregard the other. The sample spell macros use casterlevel on the left side (the side which is labeled Divine Spells by default) and casterlevel2 on the right side (labeled Arcane Spells by default) but that's just to provide examples with both.
