Yes, I know it is a game but with all the material out there on Star Trek Engineering models can be made pretty accuratily for scales of internal parts. Don't take this as Negitive as I think you did a great job so far and should continue to put the thought you did to the ship. The Windows make or break a model, because they are what gives it the scale.
Lets talk a little bit about scale. The ship well a WIP seemed as if it was going to be a much bigger ship. The Windows you put on it and then the told scale makes some things you did not quite work. Well the ship looks neat the scaling of the various items and placement on the hull now don't fit so well. Looking at the model it looks like the winows are about 2-2.5 meters tall. So I will call the average deck height about 3 meters which is good and will give no closed in feelings from anyone inside. It also means that escape pods are about 2.5 cubic meters or about 5 persons per pod, so based on that the reall max crew is about 110. Most actually all of that will be in the saucer section, as the lower hull will have to be almost all support areas. This means they will all be packed in tightly like on a Current Ohio Class Sub, or you will need less pods based on how many crew you want to carry, say about 60-80. Also it looks like you used the same window cover for all the windows without thinking about how the shape of the hull might effect there placement or appearent hieght.
So starting with Pic1 The top View
For a couple of Meters to any side of Thrusters and Engines you need room for Fuel Piping work space and a manual control room. So removing the windows from those areas helps for there to cover for that. Also since there will have to be fuel storage there The escape pods should be moved outside of the area as well as quarter area, Plus who wants to sleep near a noisy thruster. The next thing you will have to do if remove some windows for walls, bathrooms etc. So there are somethings to rethink in the placement of items here when you start to make smaller ships.
The Next one Pic2
The windows on the sloped top and bottom apear to have about a ceiling of 1.5 meters to small for a normal person to stand in, so unless they are skylights they should probably just be removed. Actually all things considered the upper half of the lower hull probably is all engineering ,and shuttle maintence, storage, etc, and probably should not have windows at all. The lower hull looks to be about 17-22 meters at the thickest section based on winow size. Now Windows on the lower half of this hull makes sense as this woulod probably be the only Rec area on the ship (no Windows would means storage, and longer missions) So escape pods on the side to bottom also make sense. The ones on the top of the lowere hull look to have very little clearance now about 3.5 x their hieght, which would make them difficult to manuver away from the ship in a hurry.
The Last one Pic3
This is just about the bridge area the 3 top structures on the saucer. With the scale you chose the upper most area the dome can only be a sensor dome. The next one down can be the bridge area and would extend into the layer below it, in the center part. The lowest one the one that actually touches the saucer looks to be about 1.2-1.8 meters tall. This limites it to being ducting and support equipment for the bridge, once again because it is not tall enough to stand in.
There is more but I think this is enough to get you thinking about it.