This film's message is more of a personal journey for the viewer rather than having a right or wrong explanation. The symbolism in the film could be interpreted on many levels, spiritual, christian, or otherwise. The significance of the smaller characters, eg. Cherita Chen should not be overlooked when searching for a meaning in it all, and most certainly will not become clear after just one viewing.
This is a film capable of asking you the ultimate question (What is the meaning of life?) without being too obvious about it. Just as everyone's perception of the meaning of life is different, so is the perception of 'Donnie Darko'. The Religious/Christian symbolism seems to be the most popular interpretation, although (agnostic/athiest) proponents of the 'karma' theory would disagree i'm sure. My advice would be to just watch (at least twice) whist keeping an open mind, and make your own connection to this masterful piece of work. Enjoy.