I like the idea of one Season 1 Engine Control Room in the saucer.
The season 2-3 engine room is the one that should be in the saucer, precisely because the dilithium crystal access on the floor would be part of a power relay tie-in between the two hulls. More significantly, in at least two episodes, the Season 1 engine room is specifically referred to as being in the "lower levels" (presumably in the secondary hull), whereas the Season 2-3 version of the set is just called "Engineering," and based on Day of the Dove, is probably on Deck 7.
I'm okay with one Main Engineering Room in the Engineering Hull. It's purpose is to control the warp engines;
In Day of the Dove, a diagram of the Enterprise is shown with red, green and yellow areas. The main areas of the ship are red, the nacelles and struts are yellow, and outer areas are green. I'm assuming that green areas are the parts of the ship that are sealed off; many are low in the ship or along edges that may be crew quarters on Deck 6. Red areas could support engineering in the saucer. The could also support engineering in the secondary hull. I don't know how to add an image here, but I'm sure someone will oblige

I also think the big red-lined, yellow circle on the bottom of hull should be significant.
That was never seen clearly in TOS, because it is the location of the model mount. It is really only more obvious on TOS-R due to the virtual camera angles used. I'm not sure if the model had this feature until it was hung in the Smithsonian, which has since been changed to a stand again.