to-date linking directly from the domain has served me well and I have achieved some nice google rankings. However, all my pages are virtually now linked direct from the domain (non sub-folders) - is there a possibility that a search engine may view this as negatively (I have some thousand pages)? The, of course there is a bit the administrative work as it is getting harder to manage all those pages using FTP.
What are the implications of using subfolders? Will search engines give less weight to pages in subfolders or the opposite? What is the best way to work with subfolders?
Also, if I decide to start using folders for some sections how do I retain the PR for the existing pages I move into sub-folders. Most of these pages are already spidered by search engines and rank well and the last thing I want is for a search engine to encounter a 404 error.