Putting it all together

I have used one system for my first book. And it was this....I wrote it as a screenplay first. Then I realised it was way too long for a 2 hour film and wrote a novel version instead. So going into the novel i knew the story plan worked.

I'm working on my second novel now, and I've gone into it with a fairly open ended storyline where I know the ending situation I want but I'm not entirely sure how I am going to get there...and then, i just plan in detail one or two chapters ahead of where I am.

It's not very scientific, and I'm sure when i get to the end, I'll be revising earlier chapters to ensure later events are pre-echoed and themes are consistant etc etc.

I think it depends what kind of novel this is Kaku.
For example, this is what I did for a recent effort that involved numerous stories coming together in a theme driven book (not published, just a bit of exercise).

I drew a tree.
The roots where the situation (say, if they all took place in London etc)
The base - my central theme
The stems - characters and their stories
I tried to ensure that every part of the tree was feeding back to its origins.
Some people can do this with arrows pointing backwards and forwards.
Some take A4 paper and draw in the middle a box with their central point in it,
then arrows shooting off in all directions.
Try to make sure whatever you decide is a good image of your story that everything is connected. Arrows going back and forth.
How can I explain this is a bit better?
Its like smoke and fire.
In every story you have your smoke and you have your fire. Smoke is naturally going to run away from fire, but if you kill your fire, the smoke eventually dissolves into the air. Try to make sure that your smoke (or smokes) are not just running away from the fire, but coming back to it (probably in the climax of your story).
Wow, that really didn't make it clearer at all. Sorry, back to tree hugging I go....

I would say, now that you know your story from start to finish, re-read from the beginning with an eye toward the plot, and characterization. Are there places where foreshadowing would fit seamlessly? Are there lines of dialogue in early chapters that can be revised now that you know your characters so much better?

I guess I'm saying this is a revision-thing. If you're too "close" to the story to trust your own judgement, put it in a drawer and let it ferment for a few months. Work on something else and come back to it with fresh eyes for the revision.

I would go looking for a fresh beta-reader who would be willing to read the whole novel.

Pieces

I just read it straight through, and if it all makes sense to me, I send it to my agent. I can't say I really ask any questions during the read through. I just trust that if there's a problem, I'll see it. If I don't, then I trust my agent will. If my agent doesn't then I can be pretty sure an editor won't, either.

I'm working on a timeline. Not just one line with everything on it, though. I made a bunch of parallel lines--one for each major character or plot line. Even one for theme development might be good.
Then I draw vertical lines through them at significant time intervals -- foreshadow this thingy, Joe gets killed, etc. The sub-climax goes in a certain place, so certain things have to come together in this place. The climax comes toward the end, so I order events accordingly, writing them in on their own places in the timeline. Then I can see how everything and everybody stand in relation to one another all the way through. Does that make sense?
This sounds so linear and technical and anal I know, but because I am chaotic, and not a linear thinker at all, it is what I need.

Of course, I would give my eyeteeth for a good beta reader.

I think you find out how to structure the story only once you have completed that first draft. If you are involved deeply in your work, as you move through it new ideas form and you are unsure as to what to do with them. Only once you have followed all the characters to the end of their development archs and tied all your loose ends are you able to know what is needed and what is not.
Novels may be read front to back, but they are written in reverse.
If you have truly finished the first draft, and you know what really happens in the end, you will know what needs cutting out and what needs cutting in.

Nique

p.s - I think lines are a great idea, and I completely understand what you mean about being a chaotic thinker and needing some order to get it right.