If you have root-level access to a hosting server, this means that you'll have full control of it. That is to say, you can set up any server-side app no matter what the changes that it'll make to the software setting on the server, and you will be able to both access and customize any kind of file, which includes system files, and change any settings. This can be done by connecting to the server as a root user which has full privileges to perform all these things and also to make other users, including users who also have full privileges. This connection can be established with a web-based graphical interface or a Secure Shell console. For safety reasons, it's recommended that you create a separate user for your daily work and use the root user only when you need to customize the server or to install software that may be required by a script-driven application that you'd like to run.