Ok can someone check this & see if I got this right:
So I got a Honedge with the nature I want with perfect Atk ivs. So my next step is to give it the Everstone & breed it with a Ditto holding Destiny Knot with 2 different perfect I've until I get a baby with 3 perfect Ivs?
Then u get a male & female by that method with 3 perfect ivs each (with some different perfect ivs) breed them with everstone & destiny knot until u get a baby with 4-6 perfect Ivs?
Also what are the odds of getting 3,4,5, & 6 perfect ivs?
I wouldn't move on to Babies after one round of breeding with 3 perfect.
Here is what I would do, given your example (I am just making up the IVs for these Dittos, but I think you will get the point).
1st Breeding Pair - Honedge (31 Atk) with your preferred nature holding Everstone + DittoA (31 HP + 31 Def) holding Destiny Knot.
Breed until you have a Honedge with 31 HP, 31 Atk, 31 Def.
2nd Breeding Pair - Honedge (31 HP, 31 Atk, 31 Def) with your preferred nature holding the Everstone + DittoB (31 SpDef + 31 Speed) holding Destiny Knot.
Breed until you have at least a perfect four IV Male and four IV Female that overlap 3 IVs; so as an example, a Male Honedge with 31 HP, Atk, Def, and Speed and a Female Honedge with 31 Atk, Def, SpDef, and Speed. Give one the Destiny Knot and one the Everstone (as they are both the same Nature now), and hatch eggs until you get one with 31 HP, Atk, Def, SpDef, and Speed.
Hope that helps!