I use a version of the Snowflake Method as described by Randy Ingermanson at: www.advancedfictionwriting.com/art/snowf...

Now, I am not preaching the power of the Snowflake, but I will tell you how a portion of the process can help with your particular issue here.

Once I have figured out the basics of the storyline, I start jotting down the scenes I want using a spreadsheet (I use MS Excel)--just one line per scene being as descriptive as I want, as long as I put down the point of the scene and any important details I want to be sure not to miss. What's nice about using the spreadsheet is that I can then take each line and move it around and sort them in the order I want them. And with Excel, I can also color code my scenes.

For example, my current story has two basic sides to it. I have colored one side grey and the other white. Just by glancing at the spreadsheet I can tell what the pacing of the book is like with regards to how long am I spending with each story. You could do the same thing subplots or any other form of organization. I also have columns showing whose POV the scene is from as well as columns telling what chapter the scene is in (although, admittedly, this column is very flexible as sometimes scenes become entire chapters unto themselves, forcing proceeding scenes to shift chapter numbers).

Hope that gives you some ideas. Best of luck!