The controller must be placed adjacent to a refinery reactor vat. Depending upon its use, it must also have adjacent hoppers to provide biomass, to deposit its product, and to provide empty fuel canisters if it is being used to produce fuel. Crafting High Energy Composite Fuel requires 840 power.
The controller can also be used to control more than one vat. To add a vat, simply build a new vat directly on top of an existing vat already connected to the controller.