If you have a "EWMH/NetWM compatible X Window Manager", and you probably do (here is a list), then you can use
wmctrl to move the program to another desktop/workspace after it is already started. VirtualBox appears to put the VM name in the Window title, so something like this will probably work for you:
virtualbox --startvm myvin &
sleep 2 # adjust accordingly
wmctrl -r myvin -t 1 # move window containing title 'myvin' to the 2nd desktop
wmctrl may not be installed by default. Install it using your distribution's package-manager if necessary (i.e.
apt-get install wmctrl on debian based systems).
Helpful for troubleshooting:
wmctrl -d lists the available desktops.
wmctrl -l lists the available windows (includes window title value).