In addition to the link provided, the Operator's Guide, starting on page 236 has similar information. When you request a machine, the New Properties option should only be available to administrators, the end users aren't available to change the custom properties. I usually use that when I'm testing things and don't want to make a new blue print, say like adding another nic, or playing with a script executed by the guest agent.
There are custom properties that perform an action, like the VirtualMachine.NetworkX.XXXXX family that dictate connections for a 2nd or 3rd (or Nth) network adapter, same for adding additional disks. Take a look at the operators guide to see what properties do what specific actions. Also know that many people use custom properties to keep track of something specific for the request (like a cost center), or to execute some post configuration that a script uses the custom properties to determine what configuration to apply.
