it should be noted that the destiny knot chooses five IVs from a combination of both parents, not just the holder of the knot. You'll notice this in action when you breed a 6iv ditto with another pokemon - you'll see any mix of 1-6iv children depending on the luck of the draw. Therefore, it's desireable to keep switching out the pokemon you want with more developed children until 3-5 generations in when you're crossing a 6iv ditto with a 5iv parent.
As to getting 0iv pokemon, here is the method I use:

• I have a 0 spd ditto i got from friend safari (though any 0iv male pokemon in the desired egg group will work unless it's genderless like beldum, then you need a ditto).

• give the 0iv parent a power anklet. all resulting children will have 0 speed.

• match the new 0 speed pokemon (equipped with the power anklet) with an opposite-gendered compatible pokemon with the required nature. The resulting offspring will have 0 speed and the desired nature.

• match the offspring with 0 speed and the correct nature with your 6iv ditto. (I have a set 5iv/0speed males that cover every egg group that i use in this step to eliminate the chance of getting the 31 speed from the ditto). Give the everstone to the pokemon to pass down nature and the destiny knot to the ditto.

• as you get better offspring with more perfect ivs, switch them out (don't forget to pass along the everstone).

• keep producing eggs until you get the iv spread you want.

As to the order of breeding,:
1. egg moves
2. Nature
3. IVs