Well it depends really on whether you want it to have some bigger part in the story.
I mean we can glance over it, but you could also incorporate it. Infact it could be one of the reasons the Empire has been on the warpath again. 

You can go the magical way, connecting it to both Ith and the Aether.

You can go Crystals> but crystals being rocks meaning land would mean you get to incorporate your floating island idea.

You can turn it into something darker all together claiming perservions in the 'fuel' for the engine. (Its people/souls)

You can even make it huge magical beasts that they have to keep hidden, thus building the ships around them.

You can also just go they're magnets and interact with the weird magnetism & gravitation of the islands themselves, keeping it Star Trek like...as in it functions just don't expect to understand flowregulators and warp core mechanics.

There could also just be someone who pilots it, like a mage there in the Empire or on board strapped to a chair with headgear on that just mindcontrols it.