I run several machines on top of Virtual Box on Debian (headless).
Here some notes I made...

Install latest version from virtualbox site

The one in Ubuntu's repo is old

    $ sudo vi /etc/apt/sources.list  

add this line:

    deb http://download.virtualbox.org/virtualbox/debian trusty contrib

    $ wget -q http://download.virtualbox.org/virtualbox/debian/oracle\_vbox.asc -O- | sudo apt-key add -  
    $ sudo apt-get update  
    $ sudo apt-get install virtualbox-4.3

Updates

Before upgrading the virtualbox package make sure the VM's are shutdown
otherwise this prevents the upgrade to run smoothly.

Shut them down via sudo shutdow -h now, or via Virtualbox admin page.
On the host machine

    sudo apt-get update
    sudo apt-get upgrade

Update Extension Pack

After this update (including virtualbox)
Make sure you update the VirtualBox Extension Pack to the same version
(now 4.3.12)

Check currently installed version with

    # VBoxManage list extpacks
    Pack no. 0:   Oracle VM VirtualBox Extension Pack
    Version:      4.3.8
    Revision:     92456
    Edition:      
    Description:  USB 2.0 Host Controller, Host Webcam, VirtualBox RDP, PXE ROM with E1000 support.
    VRDE Module:  VBoxVRDP
    Usable:       true 
    Why unusable: 

Visit https://www.virtualbox.org/wiki/Downloads and copy link behind
'All supported platforms'
Currently
http://download.virtualbox.org/virtualbox/4.3.12/Oracle\_VM\_VirtualBox\_Extension\_Pack-4.3.12-93733.vbox-extpack

So as root on host machine:

    # wget http://download.virtualbox.org/virtualbox/4.3.12/Oracle_VM_VirtualBox_Extension_Pack-4.3.12-93733.vbox-extpack
    # VBoxManage extpack install Oracle_VM_VirtualBox_Extension_Pack-4.3.12-93733.vbox-extpack --replace
    0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
    Successfully installed "Oracle VM VirtualBox Extension Pack".

    # VBoxManage list extpacks
    Extension Packs: 1
    Pack no. 0:   Oracle VM VirtualBox Extension Pack
    Version:      4.3.12
    Revision:     93733
    Edition:      
    Description:  USB 2.0 Host Controller, Host Webcam, VirtualBox RDP, PXE ROM with E1000 support.
    VRDE Module:  VBoxVRDP
    Usable:       true 
    Why unusable: 

Cleanup old installs

    # VBoxManage extpack cleanup
    Successfully performed extension pack cleanup

Fix 'not finding module vboxdrv' after upgrade

    sudo dpkg-reconfigure virtualbox-4.2 
    sudo service vboxdrv restart
    sudo service vboxweb-service restart

List passthrough USB devices

    # VBoxManage list usbhost
    VirtualBox Command Line Management Interface Version 3.1.2
    (C) 2005-2009 Sun Microsystems, Inc.
    All rights reserved.

    Host USB Devices:

    UUID: b6efd3fd-051f-48ea-9a33-e484363f19d5
    VendorId: 0x04b3 (04B3)
    ProductId: 0x310b (310B)
    Revision: 1.96 (0196)
    Address: {745A17A0-74D3-11D0-B6FE-00A0C90F57DA}001
    Current State: Busy

    UUID: 5caaa4a1-7164-4630-9593-fce070b515dd
    VendorId: 0x090c (090C)
    ProductId: 0×1000 (1000)
    Revision: 16.41 (1641)
    Manufacturer: USB

VM Autostart

    $ sudo mkdir /etc/vbox
    $ sudo vi /etc/vbox/autostart.cfg

    default_policy = deny
    vbox = {
        allow = true
    }

    $ sudo chown -R vbox:vbox /etc/vbox

    Enable autostart on the VM's you want to autostart, the machine must be stopped when doing this.

    $ VBoxManage modifyvm  --autostart-enabled on 

Install PHPVirtualBox

    $ cd ~/install
    $ wget `wget -q -O - http://phpvirtualbox.googlecode.com/files/LATEST.txt` -O phpvirtualbox-latest.zip
    $ unzip phpvirtualbox-latest.zip

    $ sudo mv phpvirtualbox-4.2-4 /var/www/phpvirtualbox

    $ cd /var/www/phpvirtualbox
    $ sudo cp config.php-example config.php
    $ sudo vi config.php

Install LinuxAdditions on VM's

Attach ISO file to DVD drive

    $ mount /dev/sr0
    $ cd /media/cdrom
    $ sh ./VBoxLinuxAdditions.sh