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If I gave my 5 perfect IV's Eevee a Destiny Knot (Eevee has 31 HP, Atk, Def, SpA, SpD, but not Spe) and had another parent (Ditto with 31 Speed IV's) breed which parent does the Destiny Knot take from? Ditto and Eevee or just Eevee? Do I need 2 Destiny Knots to increase the chance of 6 IV Pokemon? As an added note what is the chance of that 5 perfect IV Eevee (holding Destiny Knot) passing down all 5 perfect IV if bred with another (Normal) Eevee?

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The Destiny Knot randomly picks 5IVs for the baby from the pool of the 12 parent's IVs, not one in particular.

From Pokémon X and Y onward, if at least one parent holds a Destiny Knot, the baby will inherit five IVs instead of three.
This can be combined with an EV-enhancing item to ensure that one desired IV is always inherited; however, the offspring will still inherit only a total of five IVs from its parents (the EV-enhancing item simply guarantees which IV will be transferred for one of the five that the Destiny Knot allows).

Source: Bulbapedia

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Can I use 2 Destiny Knots while breeding to have "better chances" to have a 5 IV baby?
Nope, Destiny Knot does not stack. Even if it did, it likely wouldn't make much of a difference, since that means it would pass specific stats more than once, likely making it even more reliant upon RNG to determine the offspring's IVs. You're best using an Everstone on the second parent, to manipulate the offspring's nature.
Thanks, fizz.