I don't know if you've ever seen Scent of a Woman, with Al Pacino, but there are elements to your story very reminiscent of that movie. Dead Poet's Society too. Let's break your story down into conceptual terms. Your protagonist has a really tough life and his friends are the only place that he can really feel at home at all. You take that comfort away from him by forcing him to watch hes friend commit a murder. You give him a moral dilemma that involves deciding whether to compromise the only place that he feels at home. The stake is high, the tension is high. In those terms, I'd say you've achieved what you want to achieve.
Let's move past the tension into the exposition. We have a little to improve here, though not much. The first place that I'd say your exposition is less than ideal is at your introduction of Will. You force yourself into a position that does not allow you the opportunity to show the dynamic between your protagonist and your brother. The only option you allow yourself is to tell it. This, I cannot help but think is a mistake. It's enough to tell us that on the bright side your protagonist's brother wasn't home. You have mentioned Will earlier, and all we need to know at this stage is that your protagonist has feelings of resentment toward him. When we encounter Will, you have all the opportunity to show us the tension between these two. It also allows for an element of mystery to keep Charlie's relationship with Will under the wraps until it need be revealed. Leave us with the curiosity until you can do the scene justice. A brief mention to foreshadow the relationship is what you want.
The other weird thing was the room description mentioned in part 2. It seemed like some lame attempt to characterize that was completely out of place. Besides, your character has a conscience, he wouldn't notice a messy room. It seemed out of character and threw me. He's also a coward, which means that he is unlikely to go sit quietly in his room after he discovers a murder has just been committed for which he feels the guilt. He wants to be alone, most likely. He's going to mourn and then feel an intense hatred for Austin. If he eventually toes Austin's line, it's not going to be because he sympathizes. It's going to be because he's scared.
The story itself is strong, but slightly flawed. The question I think you need to ask is really how guilty Charlie actually feels. If he is as guilty as you have portrayed him, chances are he's coward enough to find refuge for his guilt by turning himself in. What you are really trying to portray is that he knows nothing will happen to him. After all, he did get kicked in the balls to save the girl. He was only guilty because he ran. What he is afraid of now is continuing to survive with no place to run. He has no friends he can trust. His father is a drunk. His brother is following in his father's footsteps. The focus needs to shift to portray this fear. Of course, he doesn't realize this yet. The guilt he experiences was born from his realization that he is not willing to face the music and save the girl at the cost of his friends. He didn't realize, they were already lost to him.
The next question is where does the story go from now. There are infinite possibilities, but remember the following things as you continue:
1) Open an escape route. An ideal for which your protagonist can grasp. This is very important in keeping up the suspense. We need to be routing for him, but if there's no visible way of escape we will lose interest.
2) Charlie needs guidance and companionship. For him to atone for his sins, he needs to be able to build himself a concrete life.
3) Your story is primarily a character story. It's focus is on the development of Charlie from coward into something more. The story needs to flaunt this character arc as much as it can.
Very nicely done. I enjoyed the story remarkably. The idea at the end of the second part is intriguing. Remember, though, don't make the mistake of many writers and let this mysterious deja vu overshadow the character story.
Hope I helped!
Yoda
Just a question; what season is it in the story? I was thinking fall, but I'm not quite sure. If that could be cleared up, t'would be great.
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so I can't tell if it's different or not. Some of the descriptions were off, and often your wording was off, but overall I think the strongest part of this was Charlie's voice. 
. I liked how your character asked future plot questions which are yet to be resolved, it makes the reader think about the plot more, so yeah, keep on doing that. Lastly, for this little paragraph thingy, I'm glad you put this in general fiction novels. Because this is going to be a Romance story, right? And if you were to put it in Romance it would be complained for having to much action and vice versa.
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