Make sure you know the name of your VM. Both options work, second just shows you which are running :
VBoxManage list vms
VBoxManage list runningvms
Let's assume the VM is called WindowsServer (if there are any spaces in the name use quotes).
To start the VM in headless mode (first option works best as it doesn't leave command line hanging):
VBoxManage startvm WindowsServer --type headless
VBoxHeadless -startvm WindowsServer
To run it in the GUI:
VBoxManage -startvm WindowsServer --type gui
To stop the VM you would again use VBoxManage but this time with controlvm option. controlvm has several options pause|resume|reset|poweroff|savestate
To stop the VM in a saved state:
VBoxManage controlvm WindowsServer savestate
For a graceful shutdown:
VBoxManage controlvm WindowsServer acpipowerbutton