The order have always used their spaceships to travel from Earth to other destinations, including their home planet. The way that they hide the ships from human eyes is quite simple. They created special cloaking devices that make their ships completely invisible when they are in the sky. They reflect everything around them in a way that makes it almost impossible for humans to see them. They also always go out only at night and they never use any kind of lights.
There is no need for external lights in any of their spaceships and the technology they use is far too advanced for humans to even comprehend. Most of the order spaceships are actually hidden in hangars in desolated areas in the main deserts and forests of the world. These hangars are also perfectly hidden from human sight, but all members of the order have underground access to these hangars.