The decks are, indeed, stacked along the ship's direction of travel so that "up" for the occupants is in the direction of the ship's "front." Originally, there was a technological rationalization for this wherin ship's gravity was at least partially derived from accelleration. Aridas
had that all worked out and it involved "banking" the acceleration forces and a number of other complicated things. For dramatic purposes, all it does is keep everyone's feet attached to the deck.
The windows shown in my latest sketch are oval in shape and taller than they are wide. I thought that was most in keeping with the ship's inspirational origins in '40s and '50s pulp science fiction. I did try orienting them the other way but didn't like the look of them.