This guide pretty much sums up everything for breeding in XY/ORAS:
http://www.smogon.com/forums/threads/breeding-perfect-pokemon-in-pokemon-x-y.3490432/
When a Destiny Knot is attached to a parent, up to 5 IVs are randomly chosen to be passed onto the egg. Those IVs could come from either parent, so it doesn't matter which one is holding the Destiny Knot. So the better IVs your parents have, the better IVs your eggs will potentially have. As you breed more eggs, you'll get some that make for better parents (i.e. have better IVs) and should swap them into the daycare. I guess you could say beginning the process is breeding for good parents.
To help get you started,
Most,
Mattapod, and
Buckert all have Ditto giveaways going on, allowing you to get Dittos with really good IVs. They each have links in their signatures to tell you how to participate if you're interested. :)