Veja o manual aqui sobre o uso do VBoxManage e a opção guestcontrol. (Especificamente 'executar')
Exerpt:
execute, which allows for executing a program/script (process) which already is installed and runnable on the guest. This command only works while a VM is up and running and has the following syntax:
VBoxManage guestcontrol <vmname>|<uuid> exec[ute]
--image <path to program> --username <name>
[--passwordfile <file> | --password <password>]
[--environment "<NAME>=<VALUE> [<NAME>=<VALUE>]"]
[--verbose] [--timeout <msec>]
[--wait-exit] [--wait-stdout] [--wait-stderr]
[--dos2unix] [--unix2dos]
-- [[<argument1>] ... [<argumentN>]]