I know there's already a question about this, but I still don't get it. To refuel the cube, you need research with tech cards. To make the tech card you need to use the cube as an ingredient, and the machine you use also needs the cube to be used as boiler fuel. The other two fuel options, phantom constituent and condensed fuel; can't be crafted from the beginning.
(Ah there's already a free recipe to reboot the cube. Nevermind.)