Like you, I'm fascinated by story structure, the hero's journey, and the mono-myth. And I've struggled with creating something less than flat characters.
I've read the Snowflake method, and parts of it definitely work for me. Another book that I highly value is Dwight Swain's Technique's of the Selling Writing. This was one of the first books that I read on writing fiction, and I still think it's one of the best. I would also recommend Baboulene's, The Story Book, for it's discussion on subtext.
Unfortunately for me, the focus on technique left me not only with flat characters but also a severe case of writer's block. However, I may have found a solution to both problems in John Dufresne's Is Life Like This? Dufresne advocates a more organic, even serendipitous, approach to story creation. For him at least, the results can be wonderful (read his Love Warps the Mind a Little, or his short stories in Johnny Too Bad), and for me, it's got me writing (finally!) and seeing my characters as something more than just cardboard cutouts. Like anything else, it's not for everybody, and YMMV.
Good luck, and keep writing!