i used MS Word for the outline and OneNote for my notebook to keep all my odd thoughts in.
OneNote became part of MS Office in the 2010 edition prior to that it was a add on you had to pay a mint for.

this is the link to the MS site for the product
i started using this for work and it took me about 3 weeks to see how it could help with my book project.
now its not for everyone and i don't make a dime for telling you about it. but it is a good tool for you to know about.