This suggests he's filling the cylinder with magickons. Where they come from, I don't know, so it's possible that Lodda has created a magickon generator. I'm not saying he doesn't have a generator, but what Jamie described sounds more like a battery to me.
The first one is the generator, or perhaps an accumulator... Like a RAM scoop (used to collect hydrogen to power a space drive). The other is the capacitor or perhaps the battery.
I would venture to say that the squat cylinder is a generator and not an accumulator. Occam's razor - Outside of this system, magickons don't (yet) exist. Destroy the generator first.
Now, are the generation components shielded? Is the control panel? Can they send magicks through their perspective without traveling there? I'd bet they can.
Regardless of how this has all been brought about, the ship is moving and they must do something. Time has run out.