Your organization is genuinely perfect. The logo is in the right spot, the nav is in the right spot, the content is in the right spot... Everything flows well, isn't off-position, or anything like that.
Your presentation is lacking, however. It's a bit busy with contrasting colors causing the eyes to not focus. Your logo/banner blends with your background, your content header is an off-color, your navigation is unreadable, and the over-complexity of it is unnecessary.
Your placement is not in question on this, for sure, you've got it down. Work on your colors/design a bit. The layout is nice, the theme is what's bad
Maybe some gfx people will be able to provide more detailed feedback as to what I mean.