Yes, there is still a main configuration file with the same structure and syntax. For your case, I would recommend installing the application builder and create a new application (for example "mynewapp") using application builder. Then close application builder, and manually move your customized configuration files from your 2.4 location, c:\inetpub\wwwroot\flexviewer (if you were using the default) to the new location, c:\inetpub\wwwroot\flexviewers\mynewapp (the default when using IIS).
You should then be able to open application builder and see your 2.5 application based on the updated config.xml.