Okay, so you thought you would have your course site complete by the first day of classes, but summer vacation persuaded you to go in other directions, or something like that. You did manage to put up enough to get everyone started, maybe on the first project or through the first exam, and you have most if not all of the policy documents posted (I hope it’s all on that point).
It’s still not too late to do a little course remodeling and as long as you make it clear to students that some changes will occur, whether in general appearance or arrangement of content or additions of content, they will be able to follow along. But as long as you are tidying up in public, so to speak, why not get some feedback from students about what they would like to see and what arrangement makes sense to them? Open an Extreme Course Makeover discussion thread and see who wants to get involved. I think you’ll be surprised about how involved your students want to be in some aspects of your course design, and the focus may actually help some students with navigation, as well as with understanding the whole course concept.