The FTL Drive and Shield Generator are integral to operating a spaceship. They allow the ship to traverse space quickly and safely. Since you will be running them off of phoron and power, it's integral to get your engines going. Better hope your Engineering staff knows what they are doing.
The FTL Drive is controlled by the Helms Officer in the bridge. The only thing controlled by you Engineers is the phoron and power to the drive. Power is connected when you get to the ship, but phoron must be connected by you. The phoron is in the two canisters directly left of the drive and gen. Wrench them onto the ports, and open the valve closest to the drive. You now have phoron running to the FTL drive! It's a good idea to ask the bridge crew to confirm that it is charging, even though the sprite is animated once phoron begins flowing. The FTL drive requires a total of 10,000 moles of phoron (which is burned during the jump), as well as 5 MW of power.
The Shield Generator is controlled by the Weapons Officer in the bridge. Again, the only thing controlled by you Engineers is the phoron and power. Setup is the same as the FTL Drive, but this valve is the closest one to the generator. Again, ask the bridge crew to confirm that it is charging, even though the sprite is animated. The Shield Generator burns between 100 kW of power and 1 MW of power depending on strength while active; and 100 kWh of power every time the ship sustains a hit to restore the shields (restores up to 10%, takes 15 seconds.) It also requires 5,000 moles of phoron to activate plus 1,000 moles of phoron per hit resisted; it can resist one hit without the phoron attached.
The greatest of Engineers upgrades both the generator and drive. Is there a way to keep you from having to go switch out plasma canisters? Maybe it would be a good idea to provide backup power, or to disconnect them from the main power net? Is there a way to get more moles from the same volume? Keep in mind, the drive and generator's tanks charge in moles, not by volume.