There are only two of those boxes, and they're both on the top. You can see them in the side profile as two slender squares rising above the profile. My guess is that the engine(s) is underneath the ship where there's an opening.
Here's an update, with a fighter for size comparison. It's not very big, but it has a lot of weapons for its size. Eight laser turrets and eight missile launchers. I guess it's the rebel equivalent to the Lancer.
[attachment deleted by admin]