If you have root-level access to a server, this means that you'll have full control of it. That is to say, you'll be able set up any server-side application irrespective of the changes that it will make to the software setting on your server, and you're able to both access and customize any kind of file, including system files, and change any settings. This can be done by connecting to the server as a root user that has full privileges to do the aforementioned things and to create other users, which includes users that also have full privileges. The connection can be established with a web-based graphical interface or a Secure Shell console. For safety reasons, it's recommended that you make a separate user for your everyday work and use the root user only when you have to customize the server or to set up software which may be required by a script-driven app that you'd like to run.