Can someone clarify a few things for me regarding breeding and EV training?
1. If I want to pass down IVs from a Ditto, I just need to give it a Destiny Knot right?
You're going to get a combination of the Ditto and the other parent. With the destiny knot, 5 ivs are taken from the pool of both parents (instead of 3 without), and the 6th is always random.
Hence the old method of having to replace a ditto/other parent to get better odds. You're still going to have to switch parents depending on how many ivs you start with on the non-ditto parent, but it goes quicker/ your odds are better of getting more of the 31 ivs instead of the other stuff.
2. When you have a Pokemon that's 5IV, the guy inside the Pokemon Center in Kiloude City would say "Outstanding..." then list which five are perfect. If he only tells you four, then does that mean a Pokemon is only 4IV?
Yep. Outstanding is just a general rule, I'm not sure how the actual cutoff works.
3. Is there any way of knowing if you've maxed out a stat apart from the graph? Or do you need to keep track of how much?
If you mean EVs, when you max a stat, it won't let you train any further, or use a correlating bag.