I have a site with different themes - and a lot of pages belonging to these themes - - so I want each theme in its special folder - only index shall stay in the root - so far all my pages are in the root ("manage projects" has no obvious subfolder management ?)
Is there a work around and will all the links in the pages automatically be corrected ?

No, this cannot be done automatically. I'd say there are two ways to go:

1. Accept the flat folder structure, and make one single index file that will be the page that opens when the site is selected. the other files are given names according to which theme they belong to, so if you have a site about films, which you obviously have, it could be for example germanfilms-about, frenchfilms-about, germanfilms-trailers, frenchfilms-trailers etc. In the navigation menu you could separate everything the way you want, so that you have a 'German Films' with submenus 'home', 'about', 'trailers'... and the same for the other themes. It would be one SD project and fairly easy to keep track of.

2. Make more than one project. For this I'll use my mock-up.coffeecup.com as an example, and it had to be more than one project simply because I'm using all the different framewoks (and non-frameworks) that you find in SD. Make a project with just one file, which is the index page, and make a navigation with links to the other projects' index files. Then make a new project for each theme, each with its own navigation and one link to the 'main' index file. You can upload it all to the same server, but make a subfolder for each theme. The main project, the one with only one file, goes into the root folder. Here you need to keep track of which project or theme you are working with to avoid havoc. It is quite easy for me because I always know which 'theme' I'm on with the different frameworks, but also here I name the various files so that I know where they belong. Better safe than sorry.

Thanks Inger - very nice ideas - the second one might fit my needs but I'm sure I will mess up all after a while.
Long ago I used Dreamweaver and that was all automatic. Perhaps I can use it again and give a new order to the exported SD files through old Dreamweaver - importing the project there and arranging all new with subfolder - whgich is very easy in Dreamweaver - and no link will be forgotten.
Do you think SD will stay with that flat structure ?

I have no idea if they are planning on restructuring SD or not.

I got a very easy way - but I would have preferred to arrange the folder structure in SD during work.
But nevertheless - here it is:
after Export I use an old Dreamweaver 8 - Menu - Site - make new site - direct to the Export folder of SD.
Dreamweaver will make a Cache of all files and after it is finished you can make new folders and drag the fileds into the folders. Dreamweaver will adjust all relative links for the new folder.
Then delete the old order on your server and upload the new one.

Why ? I have read, that Google SEO gives more attention to files in different folders ...
who knows.

Can be done in site designer but phew it requires some fancy footwork, doing it after exporting in Dreamweaver is ok but of course requires redoing it again of one has to make even small changes to the project in site designer.

In all my years using site designer instead of Dreamweaver I have only made 2 websites for my client family using that modular file system way and I have to say that in my experiences it makes not a hot of different to the performance or listings for any of them.