xvigauge, with all due respect I think you're looking way too far into the future. There are ways to produce the PDF you need -- several ways. Don't let PDF output issues determine your writing tool.
Right now I suggest experimenting with Scrivener. Believe me, it's a tool for writers. Word is a tool for just about everything and you're not getting set to do just about everything. You're getting set to write a novel and what you need are tools to make that easier.
Why not do this: download Scrivener and start the free trial. When you have it installed on your Mac, you can contact me if you like and I'll send you an example of how to use Scrivener to write a novel (or set of stories, not much difference). You can poke around in it and see how it works, what you can do. Post here if you want to do that, and I'll post a disposable email address you can use to contact me. Probably you don't have enough posts to quality for private messaging, but if you do, we can handle it that way.
When you're all done with the actual writing, you have options such as Campyguy laid out. You also have other options, such as asking somebody you know who knows InDesign to slide your final Word document (that you created via Scrivener) into InDesign, maybe make a few adjustments, and put out a fine PDF.
I do this regularly (no, I'm not looking for work right now) and a simple Word-->InDesign-->PDF job might take me an afternoon. I guarantee you that something printed from a PDF created by InDesign is going to look better than one created by Word (or Scrivener). There's a difference between word processing and desktop publishing.
There are plenty of people out there who will do this when the time comes. I did a search a few weeks ago because I was asked to do a paid job at a price that satisfied me, but I was wondering what other people charge. I saw what looked like legit operations in the $200-$300 range, and some of course much more.
But as I said -- really, this is all for later. Right now, your only job is to write that novel.
