I voted in the nacelles; because that's what I always thought when I was watching it growing up. What I saw gave me the distinct impression that the antimatter pods (which presumably contain the antimatter), the reactor and the warp apparatus were all in the nacelles. Why else would the Jefferies tube be at an angle? It goes up the nacelle pylons to get to the warp reactor.
When I got older I thought that maybe it was a bit more like the NX class (although this was way back in the 90's, well before ENT), except the reactor was really big so they had built it under the floor.
But thinking about it again now, I see no reason for it not to be like Matt Jefferies originally intended. I can even buy (just) the big red V8 powered by lightning we saw in TAS (can't think of the episode right now) being the warp reactor.
There could well be a third reactor, perhaps powering the rest of the ship when the engines are on tickover, but I'm not sure - that seems a bit convoluted. Surely impulse (i.e. fusion) powers the rest of the ship.
I think that the Engine Room we saw on screen is either right in front of the impulse deck (making the big triangle tube setup part of the impulse reactor), or in the secondary hull, about where the new cargo bay was in TMP (making the tubes some sort of power converter, perhaps taking excess warp power and converting it to mains electricity).
I don't think that it is akin to the warp control monitoring room from the Enterprise D for a couple of reasons: a)they'd be in a fairly inaccessible place, b)they'd be duplicated in each nacelle and c) there is a corridor outside that can't fit in the nacelles.
That said, I have no problem with there being more than one engine room, perhaps having an impulse one and a warp one. you'd just have to explain which you wanted to the turbo lift each time.