Wonder what's the thought behind having one type of booster for earth and one for space, since they both seem to be reaction engines.
From what little we know it seems that the primary engines are air-breathing in that air is taken in much like a jet engine.
We don't see any fuel being used (nor does there seem to be any place for this to be stored) so, presumably, it's an advanced [insert tech-babble] engine.
The basic principle is still that it requires air to be taken in and blown out for thrust. Hence the air intakes on the "front" of the engines.
There were to be larger air intakes in an earlier version of the Bubblecraft *
As for the "secondary" engines for spaceflight, again we don't know the precise mechanism or science but since the upper atmosphere / space has little or no air, a secondary propulsion is required.
Presumably, again in the absence of other information, the "secondary" engines are less powerful in atmosphere but sufficient for upper atmosphere / orbital manoeuvring.