Part of the reason for stripping down the classes to two powers each is to make them simpler, of course, and to purge the overpowered classes like Paladin or Cavalier. The other reason is to create a simple set of class modification rules, so that it's easy to get as many classes you need for your own needs without requiring extensive reference materials.
Each of the six classes has a base ability and a scaled ability. A hybrid class would take the base ability of one and the scaled ability of another. They are named thus: "Hybrid X/Y", as in "Hybrid Trickster/ Charmer", with the source class for the base ability listed first. That's simple enough; you just need a few rules to interpret the new class.
Experience and Hit Dice: Hybrids of two mundane or two supernatural classes use the appropriate HD progression; a cross-type hybrid (one mundane and one supernatural class) uses the supernatural XP/HD progression if the scaled power is supernatural. If the base power is supernatural and the scaled power is mundane, double the mundane XP progression.
Limitations: The supernatural scaled powers (spirit persuasion bonus, spell preparation/casting, and innate powers) have to be interpreted a little differently if separated from their matching base power. A Cleric without the "sense and communicate with spirits" ability has to bargain with or coerce manifested supernaturals to get spell-like benefits, so "paladin-ish" Fighter/Cleric hybrids would need to travel to a shrine or temple where a supernatural being is known to manifest in order to refresh their powers. Characters with access to Magic-User spells, but no ability to comprehend magic, can't use a spell book or learn spells on their own, but must be taught each spell by another being who knows that spell. The Gifted have it easy, since their base power doesn't really affect their scaled powers (but I would allow the base Gifted power to include crude psionic combat, so Hybrid X/Gifted classes are psychically vulnerable.)