I'm sure you will get many replies offering many different ways of writing up your family history, all of which are equally valid, so you'll have to choose one that suits you personally. For me, I like writing a narrative account, annotated where apprpriate. Having said that, I'm not sure how practical that approach would be if you're considering becoming a professional genealogist.
As far as FTM goes, the latest version of their "Smart Stories" is much better than the earlier versions - Have you tried that?