Universal Spells always use the Best spellcasting skill....
So basically a semi-spell user like the Warrior Mage would have 2 spellcasting skills
1) Class Spells -- This is Favored, used for spells from Class Spell List
2) School Spells -- This is optional, this is not Favored unless the Favored talent was used to make it so during character generation, used for spells from School of Magic that are not on the Class List
Universal Spells -- Always use the best (i.e. highest) Spellcasting skill - in this case that is most likely to be the Class Spells skill.