If you have root-level access to a server, it indicates that you'll have full control over it. That is to say, you can set up any server-side app irrespective of the changes that it'll make to the software setting on your server, and you will be able to both access and update any file, which includes system files, and change any settings. You can do this by connecting to the server as a root user which has full privileges to perform all these things and also to make other users, which includes users who also have full privileges. This connection can be established with a web-based graphical interface or a Secure Shell console. For security reasons, it is recommended that you create another user for your everyday work and employ the root user only when you have to modify the server or to set up software which may be needed by a script-driven app that you would like to run.