What is the best way to hide a command prompt window

Hidden Start, aka hstart, is probably what you're looking for. Use it to run VBoxHeadless.exe.

Console applications and batch scripts are regularly run at Windows startup and in schedule. The main inconvenience of this is that every application creates a new console window which flickers on the screen. Hidden Start (or Hstart) is a small startup manager that allows console applications to be started without any windows in the background and much more.

I use VBoxHeadlessTray. It perfectly works for me.

VBoxHeadlessTray is simple windows app that runs a VirtualBox VM as a tray icon: