Yeah, that's the problem :(
I've been reading about the breeding process in which you breed several generations until the number of perfect IVs increases, but I'm confused about one thing. How can you ever control your chances of getting all 6 perfect IVs if the Destiny Knot only allows 5 to pass down? Won't the 6th IV always be random and therefore have only a 1 in 32 chance of being perfect? Or am I missing a concept somewhere along the way?
Thanks.
If you are just blindly placing parents with one or two perfect stats in you are going to be hatching eggs for a long time. There is a trick to finding out which parents will pass down which stats, which is detailed in this guide over on the trade corner:
http://www.pokecommunity.com/showthread.php?t=312140
That process will sound tedius at first, and it will be the first one or two times you try it, but it DOES work. I took a Porygon I got off the GTS with NO perfect IV's and bred with several dittos until I had a Porygon with five perfect IV's in about a dozen or so eggs. And truthfully, anything you are breeding without a gender or that is male only is going to be a little more tedius than something
What I recommend is that you first gather a generious collection of Friend Safari Pokemon you want to breed. (For my first breeding project I chose Pan-Cham, because I knew a few near perfect males would be great for passing down IV's to two different egg groups). I started with catching about a dozen of the little guys, and bringing them to the stat checker for which IVs were perfect.
Then, put two test parents in the day care (say put in one that has both attack/deffence perfect and the other has both specials as perfect.... but make sure a total of four stats are represented). When you check the egg that came out take note if any of the stats were perfect, as that means that either 1) That was passed down from one of the parents, or 2) it may be a random perfect. However we are going to assume it was #1 here. Now, you soft reset, and change your parents around in the day care to closest match the information you just recieved. Once you have swapped your parents out for new ones, you should be able to get an egg on the first try with three perfects this way, and with a tiny bit of luck you could get four. Save, put a different pair of test parents in(your new 3 perfect you just hatched will most likely be a test parent now), and repeat the process....
You will likely need two or three Pokemon with 3 perfect stats before you manage to hatch one with four(unless you get lucky). Once you have at least one with four, and a few with three you should be able to start hatching one with five nearly every egg.(that is IF you are following the guide I provided a link to).
If you are breeding and just hoping for chance, just as an FYI, it IS possible for two parents with five perfect stats to create a baby with only three(If both parents are missing a different stat). However, if BOTH parents have the same stat missing (say both are missing speed for their perfect stat), you will mostly breed eggs with only four stats(5 out of 6 eggs), and roughly have a one out of 186 chance that you will hatch a flawless egg.
Careful use of test parents and double checking stats you can have a flawless ABOUT one out of every 30 eggs you hatch. I have so far bred two flawless, a Pancham, and a Chimchar. Just aim for five perfect every time, and the once in a while getting an extra will just be nice.