Honestly, the best way is to learn to use the Linux command line. The command line really isn't difficult and is MUCH more powerful and efficient than any GUI will ever be. Second, many people, myself included, do not like to run a GUI because it adds processing overhead and additional vectors for exploitation. If you install a GUI on your server, you can set the default run level to 3 (multi-user no GUI) and launch the GUI with startx to activate it when it is required. This can be a good compromise to have a GUI without the constant overhead.
Another common option that will probably meet your needs, and one I would consider before installing X server and a desktop environment, is a PHP based application called Webmin which will allow you to configure many server functions with a web based GUI. If you go this route, be sure to secure it properly.
