I just thumbed through my copy of "Making of Star Trek" and it puts warp engine in the nacelles.
-and-
MoST also says that the HQ for engineering is in the saucer and that the secondary hull was mostly machine-shops, fuel, food, water reclamation, and is a minimal-crew section of the ship.
Here is the thing about TMoST... it is a nice reference source as long as you read it very critically. The diagrams/illustrations are helpful, as are the memos, but the commentary throughout the book has to be cross checked.
The description of the (fictional) Enterprise is way off... but most people didn't know that so it's description was used throughout most of the 70s, 80s and 90s (including by Franz Joseph for his plans in 1974).
Other notable errors that were often repeated in subsequent decades included the idea that the (model) Enterprise was 14 feet long (with a saucer diameter of 10 feet no less).
Another misconception propagated the book is that the (fictional) Enterprise was much shorter for
The Cage and was only later lengthened. There is a memo (dated Aug. 24, 1964) talking about the Enterprise at around 200 feet in length and later commentary in the chapter about
WNMHGB saying the
"Overall length of the Enterprise was originally estimated at approximately 200 feet." People read that as it not having changed until much later in production, but all evidence points to the size change taking place in October of 1964 (before the models were built, before filming on
The Cage had even started).
Don't get me wrong, TMoST is a great book... and back when we had no better information to go off of, it was
the reference source for most of us. But today we have way better information than
Poe originally had access to, and far more time to consider it than he had (attempting to publish a book while the show was still popular).