Donne Darko is a great film, one of my fave movies and I do have the Directors Cut.
There is actually quite a considerable amount of added scenes in... I don't know if it makes it any easier to understand, although there are scenes with passages from the Phillosophy of Time but it makes a lot better.
My only complaint is that the song at the begining (Killing Moon or Head Over Heels, I can't remember) where Donnie rides his bike home is replaced by another song and moved to the Party scene. Maybe I'm use to the one in the original release been there but IMO it just doesn't work and flow as well with the new one.
My interpretation (and this is basically molded together from what Richard Kelly has said and from various other interpretations) of Donne Darko is that...
When the jet engine fell in his room, because it had no origin corrputed the flow of time and created the tangent universe which will collapse on it's self in 28 days, 06 hours, 42 minutes and 12 seconds in a black hole that could wipe out the whole of existence.
So in the Tangent universe Donnie is saved by Frank and is guided by Frank and the Manipulated Living (Dr. Thurman, Karen Pomeroy, Dr. Monitoff, Gretchen etc) to do things or to be at certain places at a certain time.
Examples...
Frank guides Donnie to flood the school so that he will meet Gretchen and start going with her.
Donnie and his friends see Grandma Death walking to the mail box, and Ronald suggests that someone should "write that b****". Perhaps manipulating Donnie to write to her, so that she is reading the letter when Frank's car swerves to miss her.
Karen Pomeroy tells Donnie about 'CellarDoor' which is a hint to Donnie to go to Grandma Deaths.
Basically Donnie must take the jet engine back through the wormhole to give it an origin and save the universe.
Donnie is laughing and didn't get out of bed, even though he knew the engine would kill him because the Tangent Universe had solved his problem of dying alone through achieving enlightenment, and subsequently he knew he was going to "something better" (from his letter to Roberta Sparrow). He was therefore laughing through sheer joy and anticipation, and didn't want to get out of bed.
For the most part no-one knows about what happened in the Tangent Universe except those during the Mad World montage who seem to remember, who also turn out to be most of the Manipulated living or Manipulated Dead (Frank).
http://www.tonystuff.co.uk/darko-spoilers.htm#top- Page of theories/explanations
The Philosophy of Time Travel- Good page. This page basically just gives the info available to us from the Philosophy of Time Travel. And it all basically back-up the interpretation I just wrote, which is why a lot of people go for it, although Richard Kelly has said that there isn't one 'definitive' interpretation.