The easiest way to start an program is by running the program of your choice (VirtualBox, VBoxManage, or VBoxHeadless) from a terminal. These are symbolic links to VBox.sh that start the required program for you.

Alternatively, you can directly invoke the required programs from /opt/VirtualBox. Using the links provided is easier as you do not have to enter the full path.

You can configure some elements of the VirtualBox Qt GUI, such as fonts and colours, by running VBoxQtconfig from the terminal.