no, that isn't what's happening at all (in reference to all posts above jolteon's explanation)
you pass down three IVs from the parents of your pokemon. you chain breed IVs to get triple flawless, that is best you go for systematically.
basically do it like this: if you want a metagross with flawless attack/defense/hp (my personal recommendation but speed is still okay i guess), then breed beldum with ditto number one that has flawless attack. go until you get a baby with beldum with flawless attack, now, switch out ditto and old beldum with ditto that contains flawless defense, and beldum with flawless attack. breed those two until you get a baby with flawless attack and defense, then swap out both again, this time for ditto with flawless hit points (and it helps if you have a ditto with the right nature so you can attach an everstone to get the nature passed to the child 50% of the time) and switch in your double flawless beldum. keep breeding until you get one with flawless hit points, attack and defense. it's quite time consuming but well worth it in the end. the other three IVs are randomly assigned, so you could feasibly end with more flawless IVs, but it's unlikely.
the stats DO NOT increase because you breed, you can't breed 100 times and get flawless IVs across the board, they are randomly assigned for three stats, and inherited from the parents (stat and parent are chosen randomly as well). you could get wonderfully oustanding on your first egg (as i did with my bagon, though it didn't have the stats in the right places or the right nature), or you could breed endlessly (as i did with my exeggcute and had to settle for a double flawless one) without much luck.
using the breeder, you're looking for at least quite impressive in ability, if not wonderfully oustanding (wonderfully oustanding is the best).
beaten... oh well still helpful i guess