HBassman, one of the nice features of LR is that your actual physical folder layout on disk isn't that important. Since LR uses a database to point to your files, wherever they happen to be, you can find and organize your photos however you wish, regardless of how they happen to be distributed on your disk.
Example: you don't have to group your photos by topic or subject on disk, since by keywording in LR you can easily find all photos of a given subject. Let's say you photograph birds, and you want to find all of your Brown Pelican images. Well, even if you have Brown Pelican images strewn about all over your hard drive -- or perhaps multiple drives -- it doesn't matter as long as each image has a "Brown Pelican" (or similar) keyword tag. Once you're in LR, you just type in "Brown Pelican" into the Find box and suddenly they're all there in front of you.
Same thing goes for finding images by date, location, or just about any other criterion. The main point is to have your images diligently keyworded, so that you can find them quickly by subject or location. (Things like date and camera model are less important, since these are automatically tracked via the files' EXIF data.)
It doesn't hurt to have some system of organizing files on disk -- I use a simple date system, e.g.
2007/2007-09/raw/MG_9185.CR2
(year, month, "raw" folder, files)
But the exact organization on disk is not so important if you're making full use of LR's built-in organization ability ...