Atonement

I'm trying to think my way through something and I might be way off base.  Part of the problem is using faulty analogies to describe the whole atonement, when I believe atonement is layers and layers of saving grace.  You may ask why I'm fretting over analogies when I know the answers.  I'm not sure.  Maybe I just like to fret and make things harder than they are.
The first analogy is the nail in the board.  The story consists of a person hammering a bunch of nails into a piece of board.  The atonement not only clears the board of the nails, but polishes it back to a smooth sheen.  I get it.  Where I question it is this:Yes. Our (true) repentence = immediate and complete forgiveness from Heavenly Father. But (in my way of thinking) it's not as though the act/sin was never committed. It was. The words can't be unspoken. The hurt can't be undone. Some losses simply can't be given back. That's why repentence is hard and involves a serious change of heart. We have to never want to go back there again because we understand that the wounds that we inflicted on others, on ourselves, on Christ as He atones for us, damage our spirits.   Our hearts have to change so profoundly that our actions reflect this change.  That's why (for mere mortals) forgiveness can be hard. It takes a lot of humility on both sides to accept that Heavenly Father will judge righteously. It takes a lot of strength for someone to say "You took this from me and you can't give it back, but I'm willing to let it go and let someone else sort this mess out." 
The second is the pit analogy.  You are in a deep pit and have a ladder, but the ladder is too short.  So you climb the ladder and Christ comes down and makes up the difference, thus enabling our works to be accounted to our gain.  But here again, I think we misunderstand.  The atonement is infinite and eternal.  Christ descended below all things.  He went deeper than our pit and saved us the entire way up.  Our works, our fulfilling of our covenants and then enduring to the end are our necessary part of being saved; but they don't save us.  Christ did.  Like King Benjamin says, we are unprofitable servants.  Nothing we could ever do would ever make us close to the same level as Heavenly Father.
And then there's the lesson of the Prodigal Son.  The father joyfully receives the son back to the family, but the inheritance is gone, lost, squandered.  Some things can't be given back.  Look at David.  One (rather large) misstep and he lost everything, even though he repented and continued to spend the rest of his life serving God.
And the workers in the field where the early morning workers earn as much as those hired just before quitting time.  The reward is the same no matter when it is earned. 
Ahhh!  I know Christ's parables don't conflict with each other, unlike some of our modern analogies.  My mind is trying to wrap itself around an atonement that heals completely (which I totally believe in) and my finite understanding of God's justice.   Here's what I'm thinking.  Heavenly Father doesn't need to look at our sins once we've repented of them. He remembers them no more. We don't need to remember them to hold over ourselves in condemnation, but we do need to remember the consequences of sin. Nothing we do is in a vacuum.  Our choices have serious consequences that radiate out like ripples for generations.  I think the only way that the board becomes whole again is if all parties involved use the atonement. The sinner becomes clean through repentance. If anyone was hurt, they become healed also through the atonement. 
Maybe the Prodigal Son and the Hired workers deal more with exaltation rather than salvation.  We can lose our exaltation.  There is still a reward which we will rejoice in, but it may not be the full inheritance.  Exaltation can also be granted at any point on our journey.  As long as the covenants are made, kept, and lived it doesn't matter when exactly.  Although, how much better to live with them sooner rather than later.
I thank Heavenly Father for the opportunity to repent and to become clean again. I want my kids to understand that they can and will make mistakes. I want the atonement to be real for them. I want them to know that Heavenly Father loves them no matter what they do, but that he expects them to not stay stationary. I also want them to understand that it is so much better to do what is right and that as they grow closer to their Savior, the desires to do wrong will diminish. 
I hope to have a better grasp on these concepts myself.  Feel free to chime in.