The secondary class rule is a variant rule of the variant gestalt rule. Instead of getting the best features of both classes, you add only the class features of the secondary class. Your secondary class is always half of our total character level (rounded down).
Your secondary class automatically advances as your total character level advances.
Quick and dirty, might have to look at the base classes and shore up some of the classes that have less class features against what is gained with some of the classes with the most attractive class features. Perhaps getting bonus hit points for classes that don't have class features at every level or don't advance in spell-casting (mainly thinking of fighter).
Well that seems clear enough, it's half character level. So if you're a 10th level Fighter with a secondary class of Wizard, you would have the spells and class abilities of a 5th level Wizard.
Pet piev: caster level and spell are class abilities, always have been. Once you start thinking of them as x/day variable spell-like abilities, they really stat standing out for what they are.