When first starting a lightroom catalog.. I first manually move my folders to the location I desire trying to keep a logic to the folder structure which stands alone from lightroom to make manual tasks easier. Everyone has different needs, but I start with a folder named Images, then Year, then Location, then Date. Lightroom on import, builds the indexes and previews fairly quickly (much depends on the speed of your machine and the drives) so I wouldn't hesitate to start clean. Even importing 100,000 images might only take a few hours..
Lightroom is fully capable of supporting hundreds of thousands of images in the same catalog, though there is a point where you'll want to dedicate a fast drive just for the index/preview images.