All the setup and blogs are stored in xml files under app_data folder as shown in the image. When I do administrative set up or new blog, it will be written on the webserver but I have my project in the TFS and next publish to the webserver will overwrite those changes. I know that there is an option that dont publish app_data but it means that my latest app_data version will never be in the Tfs but in the server. I wonder if there is anyway to syncronize this issue beside doing it manually.
You need to do a get (copy app_data from live to TFS) before you make any edits.
You would be better using a host that supports Git as a content management solution. You can then just sync and merge like you would with a branch.