I don't think Joseph Smith understood the content of the Book of Mormon very well. Before anyone calls me a heretic for saying that, let me explain.
By not understanding it very well, I mean ONLY the actual content of the BofM. Much of what was taught back then about it was more generalities than specifics and doesn't really match the text very well - as it would have if he had studied it rigorously - or been like most authors and knew it inside and out. Ironically, his apparent lack of textual understanding of it is one of the things that leads me to accept that he translated it rather than having written it.
If we accept his general statements about visitations / visions, it seems to me that he learned some very basic, general things about it and the people it describes - but it doesn't appear he got an in-depth "tutorial" on it. In other words, it appears Moroni told him a few broad, sweeping things about the book and the people, but that most of the time they spent conversing each year was dedicated to other things he would need to know to magnify the overall calling God was giving him.
Personally, with what I've been able to glean about him and his personality, I just don't think he cared much about the Book of Mormon as a religious proof text - so he didn't study it intently to create / restore the core theology of Mormonism. I think that process was "other revelation" driven. I believe this for one major reason:
Frankly, most of the "heretical" doctrines of Mormonism aren't in the Book of Mormon and/or Pearl of Great Price. Many of the more "advanced" teachings are in the Doctrine & Covenants, but most of the truly unique concepts were taken from interpretations of the Bible - which is why, I think, Joseph once said that the main difference between Mormons and Protestants is that Mormons believe the Bible and Protestants don't.
I think he was MUCH more interested in re-establishing what he viewed as a pure Biblical theology than in using the Book of Mormon to do so - and I personally think that is pretty much indisputable. I think he saw the Book of Mormon as what some ancient prophets thought and taught, but I think he viewed its purpose MUCH more as a second witness of the Bible (as is stated explicitly in the book itself in at least two places) and a witness of his calling (as it was used in most early missionary work) than as a primary, doctrinal proof text.
I like that view, since I think it fits the book itself much better than using it to prove doctrine.