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When prestige classes advance the primary class features of their base class, they continue the CP cost progression of that base class.
For example, if Wizard advances into the Loremaster prestige class, then each level of the Loremaster class has the same CP cost as though the character had advanced in another level of Wizard. This is because Loremaster advances spellcasting, the primary class feature of Wizards.
When a prestige class doesn't advance the primary features of a class, you instead price it as though it were a new base class of the appropriate tier.
For example, if the Dragon Disciple prestige class didn't advance spellcasting or grant ability score increases, it would be the equivalent of a tier 5 class. So a Sorcerer taking her first level of Dragon Disciple would only need to pay 1 CP (or 2 CP if they've already taken three classes, see multiclassing above). The next three levels advance spellcasting, so they'd cost the same CP as if she was taking additional levels of Sorcerer. The 5th and 9th level also don't progress spellcasting, so she'd only need to pay 2 CP for each of those levels. Ability score increases are handled separately, see the answer below. She'd still be allowed to gestalt Sorcerer levels with those dead levels of Dragon Disciple, but in that case she'd pay both the CP cost for the Dragon Disciple and the Sorcerer (so 2 + 16 CP for the 5th and 9th levels).
For example, if Wizard advances into the Loremaster prestige class, then each level of the Loremaster class has the same CP cost as though the character had advanced in another level of Wizard. This is because Loremaster advances spellcasting, the primary class feature of Wizards.
When a prestige class doesn't advance the primary features of a class, you instead price it as though it were a new base class of the appropriate tier.
For example, if the Dragon Disciple prestige class didn't advance spellcasting or grant ability score increases, it would be the equivalent of a tier 5 class. So a Sorcerer taking her first level of Dragon Disciple would only need to pay 1 CP (or 2 CP if they've already taken three classes, see multiclassing above). The next three levels advance spellcasting, so they'd cost the same CP as if she was taking additional levels of Sorcerer. The 5th and 9th level also don't progress spellcasting, so she'd only need to pay 2 CP for each of those levels. Ability score increases are handled separately, see the answer below. She'd still be allowed to gestalt Sorcerer levels with those dead levels of Dragon Disciple, but in that case she'd pay both the CP cost for the Dragon Disciple and the Sorcerer (so 2 + 16 CP for the 5th and 9th levels).