Ok at some point you will want to upload files using Drupal's user interface. By default ftp is usually an option but its better to use SSH for the added security. To do that we need to add the ssh libraries to php. This is very easy to achieve as its an install and forget setup that only requires a server restart. Run this command
sudo apt-get install libssh2-php
Once installed you will need to restart Apache to make the configuration take effect. Run this command
sudo service apache2 restart
Now when you try to upload anything to the server you will be given a pull down box with options for ftp and SSH.