We are usually familiar with FTP when we transfer files from our computer to a shared web hosting service. With VPS, it usually have an ssh server that's why we can log in to a terminal. The ssh protocol supports transferring of files called Secure copy (scp). We can just reuse this service and there is no need to install a new program to your VPS.
The LAMP Stack (Linux + Apache + MySQL + PHP) is popular setup for hosting dynamic websites. I prefer to use LEMP (Linux + Nginx + MySQL + PHP) because I find it easier to install and more friendly to system resources.
Only basic commands can be done in your VPS control panel. To really use the full potential of the server, you need to log in to it's command line. From the command line, you can do many things such as: install software, modify configuration, and manipulate data.
Buying a VPS is not trivial. There are many things that you need to consider. This section will guide you in making your decision, and will also walk you through the steps when signing up with a company.