It sounds like your site might be missing its .htaccess file. This often gets missed as it is hidden by default on most operating systems.
You should still be able to login to WordPress. If you can head to Settings -> Permalinks and re-save your configuration. It will then either re-create the .htaccess file for you or generate the code that you will need to place in your .htaccess file.
Alos noticed that the pages at the main site work when accessed trough the wp dashboard and the permalinks have been set to default however all of the sub sites gives me 404 cannot even access their wp admin. The pages from main site goes back to 404 when i set the permalink to postname as well.