I'm not sure if I'm following exactly what you're saying, but here's what I got out of it.
The man that is on his way to death row for murder has several personalities, and everything that goes on at the hotel is just going on in the guy's head. Each person at the hotel represents one of his personalities. One of the personalities is the one that makes him kill.
However, the people at the hotel don't realize this; they think they are just normal people, not just something going on in the killer's head. That is, until John Cusak figures it out. So he thinks Ray Liota's character is the "killing personality" and kills him, getting shot and killed himself in the process, leaving only Amanda Peet alive. Since she is harmless, the man on death row is no longer a killer because the personality that caused him to murder is now dead.
But as you learn at the end, it was all a ploy by the kid personality (who was actually the personality that made him kill, not Ray Liota, and who faked his death so the doctors in real life would think the man was now only had the one "safe" personality left) to get him off death row. So once he is being transported to the mental ward and is off death row, the kid kills off Amanda Peet, leaving only him, the killing personality, left. That's when he kills the people driving him to the mental ward.
Kind of confusing, I know. Hope that helps.
