Different types always stack.
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You mean this for "tiers"?
Incandescent Blue Sphere (Ioun Stone)
Aura strong varied; CL 12th
Slot —; Price 8,000 gp; Weight —
DESCRIPTION
This stone grants the wearer a +2 enhancement bonus to Wisdom.
Cracked: This stone grants a +1 competence bonus on one Wisdom-based skill. Price: 200 gp.
Flawed: This stone grants a +2 enhancement bonus to Wisdom and a –2 penalty on Perception checks. Price: 7,200 gp.
See Inferior Ioun Stones for details on cracked and flawed variant stones.
CONSTRUCTION REQUIREMENTS
Craft Wondrous Item, creator must be 12th level; Cost 4,000 gp.
Flawed and cracked ioun stones were introduced in Pathfinder Chronicles Seekers of Secrets, you can find them here. some are interesting, several are too good for their price. The balance of the inferior ioun stone is wobbly.
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As Blackstorm said, different bonus types normally stack. For example, if you had +1 morale bonus, +2 luck bonus and +1 competence bonus on your attack rolls, it would all add up to +4 on top of everything else (BAB, ability score modifier, weapon bonuses etc.).
As for these Ioun stones, I'm not sure how that 'cracked/flawed' thing works (and I'm too lazy to look it up at the moment).
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Those are three different items. The normal, full-power stone, a cracked stone (usually damaged in manufacture), and the flawed stone.
The full-power stone gives an enhancement bonus to the Wisdom ability score. Your actual wisdom, and that gives you a one higher wisdom modifier. Much like a headband of inspired wisdom +2.
The cracked stone gives a +1 competence bonus to one wisdom-based check. Such as survival or perception, which are wisdom based skills. Choose one when you get the stone, unless it was already decided.
The flawed stone gives you a +2 enhancement bonus to wisdom, as the full-power stone does, but you also take a -2 penalty to perception with it. You have to decide if that penalty is something you want to deal with. A cleric might think it worth it.
Now, you can have multiple stones, but the full-power stone and the flawed stone both give an enhancement bonus to the wisdom score. So those bonuses do not stack.
It's from the same source, so it doesn't stack.