So I were to have Dominate Person (5th level spell) selected for both of these.
Preferred Spell
Benefit: Choose one spell which you have the ability to cast. You can cast that spell spontaneously by sacrificing a prepared spell or spell slot of equal or higher level. You can apply any metamagic feats you possess to this spell when you cast it. This increases the minimum level of the prepared spell or spell slot you must sacrifice in order to cast it but does not affect the casting time.
Spell Perfection
Benefit: Pick one spell which you have the ability to cast. Whenever you cast that spell you may apply any one metamagic feat you have to that spell without affecting its level or casting time, as long as the total modified level of the spell does not use a spell slot above 9th level. In addition, if you have other feats which allow you to apply a set numerical bonus to any aspect of this spell (such as Spell Focus, Spell Penetration, Weapon Focus [ray], and so on), double the bonus granted by that feat when applied to this spell.
So if I were to burn an 8th level spell slot to cast Dominate Person, Spell Perfection would trigger adding Quicken spell, but then I could still add annother metamagic ability to the spell as well due to Preferred spell and burning a higher slot.
Does this mean I could add Quicken spell (from Spell Perfection) and say Persistent spell to this Dominate Person?
The only thing preferred spell lets you do is cast a spell spontaneously and apply metamagics to said spontaneous spell w/o making it take longer to cast the spell.
This means that once Spell Perfection has been triggered you've already made all of your applicable decisions for preferred spell. As a result preferred spell doesn't allow you to get around the limitations imposed by Spell Perfection.
So, in your example. You would spontaneously cast Persistent Dominate Person (a 7th level spell) using an 8th level spell slot. You would not be able to apply quicken to it because this would add 4 levels. When it comes to Spell Perfection, the spell slot used doesn't matter it's the level of the spell that matters and 7+4 > 9 making it an ineligible option.