In addition to using skills for combat, we're now also using skills for spellcasting. Each school, subschool, domain, and subtype now has an associated Spellcasting skill, with additional skills for certain caster types (cleric, druid, paladin, etc), with the appropriate skills being in-class (ie clerics get Spellcasting(cleric) plus their two domains, but don't get any of the arcane schools, etc). Each spell now lists a Required Skill Ranks entry, and a Synergy Skill Ranks entry. Additionally, skill ranks are used for things like range, damage die, etc.

• You have one "slot" plus one for each 2 ranks you exceed the minimum required ranks, using your highest spellcasting skill. For example, if the highest spellcasting skill is Spellcasting(Transmutation), then someone with 19 ranks in that could prepare 1 spell with 18-19 ranks, 2 spells with 16-17 ranks, 3 spells with 14-15 ranks, 4 spells with 12-13 ranks, 5 spells with 10-11 ranks, 6 spells with 8-9 ranks, etc.
• For other spellcasting skills, you can't exceed the maximum prepared you'd have in that skill. For example if you have 19 ranks in Spellcasting(Transmutation) and 9 ranks in Spellcasting(Conjuration), then although you can prepare up to 6 spells with 8-9 ranks, only one of those can be Conjuration. This doesn't apply to daily spell casting for spontaneous casters, but it does apply to their spells known.
• All spellcasters use the same rules above for determining "slots", but they mean different things for different characters. For example, a cleric prays at dawn and can fill up those slots with any spell on their list, while a sorcerer would use the same slots to determine both spells known and spells cast per day, and a wizard would use them to determine only the number of spells at each level he can prepare per day (because his "spells known" depend on his spellbooks).
• Spells may also require Spellcasting(Universal). In that case, the spellcasting skill from any of the arcane schools can be used, and the spell is treated as if it were from that school, so it should be noted what skill is being used when the spell is prepared.

• Required ranks are now 1 plus 2 times spell level in the spellcasting school. So Disintigrate would require Spellcasting(Transmutation) 13 or Spellcasting(Destruction) 15. Spells only have schools, domains, or classes as required Spellcasting skills (eg, Cleric, Destruction, Transmutation, Bard, etc) but never subtypes or subschools (eg Fire, Glamer, etc).
• Spells that do 1d6 per caster level should instead probably have a DC 15 Spellcasting check and they deal 3 damage for each point that the result beats the DC. This would mean a 1st level specialist normally deals 6 points of damage (2d6 is 7 average), and an 11th level specialist normally deals 42 damage (12d6 is 42 average).
• Spells with a type or subschool listed (eg fire) now get a synergy bonus such as: if you have more than 13 ranks in the synergy skill, roll a DC 15 synergy check and deal +1 extra damage for each point that the result beats the DC. An 11th level fire evoker would usually deal 56 point damage instead of 42. Another synergy bonus might be a +2 increase to DC, or a 10% increase in range or duration, etc.
• As a simpler alternate of the above, you could use the rule that a character gets a +1 bonus to their primary casting roll for every 3 points that they beat their synergy DC. That would let an 11th level fire specialist normally add 4 to their roll, which would add 12 to their damage for fireball and similar spells. This would let you simplify rolling during combat by having them roll for synergy bonuses as they prepare spells and continue to use that roll until they prepare spells the next day.

• A spellcaster can use two slots to prepare a spell at will by making a skill check at 15 + twice the required skill ranks. If the check fails, the slots are still considered used for the day. Both spontaneous casters and prepared casters would prepare their spell slots in this fashion, and they can both do it at any time during the day, as long as those slots haven't already been used. Any spells prepare this way also have a 50% penalty to the spell casting check result (they deal 1/2 damage, last 1/2 as long, etc. similar to having 1/2 the caster level of the old system).