What that sink/source terminology really sounds like is making 'em cigars a sort of space jet engine: suck in space at front, spit out space at back. Or, more accurately, giant pole magnets of some sort.
Wasn't the nacelle intended to be explicitly bipolar at one point? That is, after the pilot, the aft end received a spherical feature - wasn't that supposed to glow, too, forming a pair with the front dome? (The side glow was another feature scrapped because of wiring problems, or in this case delayed until ST:TMP)
As for Kirk's litany in "The Apple", it very much sounds to me as if he's giving a list of escalating options, in ascending order of severity and complexity. That is,
1) Direct power to impulse
2) Dump warp nacelles
3) Crack out with main section (either saucer or engineering), leave secondary section (either engineering or saucer) behind
It's far from said which half of the ship's hull would be considered "main" at that stage of making the show, although the in-universe is pretty clear in retrospect.
Timo Saloniemi