This may sound like more work than your interested in doing, but that's what writing a full length novel is all about. If this is a creative story, which I would assume it is, this is one of my approaches when I plan to write a long piece with a solid orginization.
Take what you have, and make an outline of what you already have. It will look something like this. Keep the outline as brief as my descriptions to leave room for alterations and additions.
I. First action/important part.
1. Something that happens in relation to your important part I
a)Something that's smaller than 1 still dealing with the first important part.
b)Another smaller thing dealing with 1
2. Something else that deals with important part I
a)Something that's smaller than the above still dealing with important part I
b)Another smaller thing dealing with 2
3. Something else that deals with important part I
a) Something that's smaller than 3 still dealing with important part I
b)Another smaller thing dealing with 3
II. Second important part
1. Something that happens in relation to your important part II
a)Something that's smaller than 1 still dealing with the important part II
b)Another smaller thing dealing with 1
Thats the basic outline for orginization I used. You can also apply this to long essays. You can always use 1,2,3,4,5 and ect. if you have more ideas for each important part, and a,b,c,d,e and ect. if you have more for each of those sub categories. And obviously you can have as many important parts as you need. Once you construct an outline like this for what you already have written, do not write anymore of the actual story until you finish your outline. Obviously don't use "important part, something to do with important part I" fill those in with a small bit that has to do with your story. For example, this is an outline I have for a novel I am currently writing.
I. Giovanni Kills his best friend
1. Motive
a)It's his obsession
b)He's psychotic
2. Before he does it he says he killed his best friends fiance two years ago
II. Take story back before Giovanni kills his best friend, but after he killed the fiance.
1. Conversation between the two friends
a)Show the reader their occupation through their conversation
b)Show the reader John's (the best friend) emotions toward losing his fiance two years ago
c)Show both characters personality in the coversation
That's not my exact outline, I just made that up because I can't open my original outline right now which I have no clue why, not good -_-
Usually these outlines, if done right, end up being as long as the story itself, sometimes longer and sometimes shorter. This is easier than writing the whole thing out because, although it takes time, it's easier to change. Instead of deleting that whole conversation because it didn't display the aspects of those two characters, I could just change the outline. Make sure you re-read the outline several times before you start writing again, and as you write go piece by piece with the outline. Hope this helps, it doesn't work for everyone but it helps a great deal for me and some other writers I know. Good luck!
Also this site didn't indent like it was supposed to. I am going to indent using //// instead of spaces so you get a little better of an idea.
I.
////1.
///////a)
///////b)
////2.
///////a)
///////b)
II.
////1.
///////a)
///////b)
////2.
///////a)
///////b)
III.
So on so forth. A lot of people are saying some okay ideas, but some people are saying just write it. For many writers sometimes that works well but even for them writing long pieces that way requires far more revision than doing it this way or another well orginized way of writing. If you're planning on writing a 300 page typed double spaced 12 point font story, than you probably will find this a hell of a lot easier than just plain writing it, in the end. When I first started writing I only wrote short stories, and I made attempts at novels but stopped 40 pages into it because I lacked this outline. Once I was showed this, let's just say I have about 3 novel length pieces I am proud of and a ton of lengthy short stories I adore. Good luck with your story!