Imagine this....

You get a thorn stuck in your foot, and it hurts,
but you keep walking because you have a ways to go,
after a while it doesn't really hurt that bad,
so you leave it.

Then you begin to realize that it is still there,
the aching becomes noticeable again,
so you begin to pull the thorn out,
as you pull, it hurts,

but it is a good hurt, because you know that soon the
pain won't be there anymore.
After the thorn is removed,
the spot where it was still aches occasionally,
but not as bad as it once did, and a little while later,
the pain just kind of disappears.

You remember where it was and what caused you to be in pain,
and now you know to look out for thorns.

I think the atonement is a lot like this.