SD does indeed keep all the pages of a project (.rsd) file at the same level. I regard that as an advantage, and not as a disadvantage. It reduces the potential complexity of the program.
I use the procedure mentioned in Inger's first post in this thread. It probably wouldn't be worth it for just 50 pages, but I use the procedure because the number of pages in my site is well in excess of the 125 page limit of an SD project file.
For just 50 pages I would be inclined simply to use SD's Page Manager to set the .html file names and the order of them in such a way as to make it easy to navigate to any particular file while working in the SD project file. For example, all the file names in the Product category could start with 'prod-'. I may be wrong, but I assume that ease of navigation while working in the project file was the reason for the hope to have each page in its designated folder.
Inger's procedure is easy, especially if one
1. uses the Windows OS which allows multiple SD project files to be open at the same time;
2. uses the whole-page Component technique (mentioned in
https://www.coffeecup.com/forums/site-d … e-website/ ) to transfer page layouts from one SD project file to another;
3. lets each of the SD project files keep its own CSS and image etc. files, and doesn't complicate things by trying to have a common CSS file or image folder for the whole website (I don't think that a bit of duplication hurts, and my aim is simplicity).
Frank