If you've chosen the Spellcaster array as your type of NPC, then choose Spell-Like Abilities as the type of spellcasting it gets (rather than normal spellcasting). If you're just adding a couple of SLAs to a monster that's a combatant or expert, then go to the "Adjustment Special Abilities" table near the bottom of the Customize Race tab, and add "Secondary Magic" - then add the SLAs to the Secondary Magic table that will pop up.
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