Can I put in a vote for structure? I wrote a book last year and found it really useful to start by thinking about the book structure overall. It doesn’t need to be a complete structure, but starting with an outline of the principal ideas that the book is going to cover does no harm at all. A big advantage of this top-down approach is that it provides you with some convenient buckets in which to pour your ideas as you have them. This works well for me as I don’t think in a particularly linear way, and often found while working on one chapter that I had an idea of something to add to a completely different part of the book.
Structure and formatting are often confused, not least because of word processing systems like Word. There is nothing wrong with considering how a chapter will break down into sections and subsections, and you ought to be able to do this without assigning fonts and indentation and so on.
Incidentally, regarding tools, I have to include a plug for Scrivener. This is a Mac program (though wow, I see that the Windows version is currently available in beta - http://www.literatureandlatte.com/scrivenerforwindows/) that is designed specifically for writers. I suppose one of the things I like most about it is that it allows me to work in the kind of structured way described above, but still has a lot of flexibility in how you write. It also gets out of the way when you want it to with a full screen mode, letting you focus on the words without a lot of page furniture to distract you.