That is very impressive! Very cool. You could make your own "Enterprise tour" with this.
However, yes, main engineering is in the secondary hull (or engineering section) and is located dead center between the warp engine nacelles.
<treknerd>There are several reasons for this location as far as Treknology is concered:
1) It allows for the ejection of the warp core through a hatch at the bottom of that secion, and...
2) It allows for the ejection of the anti-matter (anti-deuterium) pods, also located at the bottom of that section (the matter/deuterium pods are kept at the top of the core, so both matter and anti-matter can be injected at opposite ends and then meet the dilithium crystal in the middle of the core, which then focusses the reaction and the plasma energy stream is created, which, in turn, is necessary to power the warp coils within the engine).
3) If te warp core were in the 'neck' that connects the two sections, it would be right in the way of the torpedo launcher and loading system, plus you would have to have much longer plasma transfer conduits that transport the high energy plasma to the nacelles.
Here is a Doug Drexler cut-away schematic as an example (so I'd consider this official):
That design concept is consistent throughout the entire Star Trek franchise and all starship designs that are Starfleet based have this or a similar layout. One further reason is, that most ships that have this kind of "saucer + engineering" design, can jettison the saucer section in case of emergency (via explosives) and use it as a life boat. We haven't ever really seen this (except in "Generations", but the Galaxy-class had a native saucer sep function).</treknerd>
Still though, awesome detail. Very nice work!