After meeting up with the Green family, they had a plan in place. They were a lot more confident moving around the ship, as well as heading to the right location, because the mastermind that was behind it all, was none other than Logan.
With him on their side, he could change cameras, turn off sensors, and work his magic behind the scenes. On top of all that, they were now with Jake as well. He had specially prepared a special power that could be used to cloak the others, and that's what they had done.
Their footsteps would still make sound, and if they crashed into someone their bodies would still touch, but at a glance, most would be unable to see them. Although there were other ways to be found out.
Because of all of this, the group couldn't always run to the location they needed to. Although at times, they did use Shiro's teleportation powers to move between floors when they checked the area was clear.