The most common attack to servers is to brute force guess your password. An effective way to counter this is to disable login via username password. An alternative way to login after doing that isto use ssh key pair login.
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.