The design of the starship is not going to be finalized as soon as I complete it. Instead, I'm going to build the prototype and call it version 0.1. As people walk through it and come to understand it, I will be open to any suggestions they have. If it seems good enough and practical enough, it will be included. The revisions may be minor or major, and the final version of the Elohim may look quite differently than what it started off as.
Now that I have made a good list of what rooms and components will be on the ship, I need to figure out what goes where. I'm going to borrow from the Enterprise-A model and stick things like crew quarters and command section near each other, while the engineering section and the shuttlebay will be toward the bottom of the ship.
There is another challenge that doesn't exist with the Sovereign and Enterprise-A ships. Remember, Elohim splits into three subhulls. This means that some things will appear more than once while others won't. Like, each subhull is going to need its own computer core (and I may try to find a way so, when the ship is in one piece, they all connect into one big core but are modular for when separated) but in likelihood only Cain will sport a shuttlebay.
I'm not new to designing starships. When I was younger and had the free time to unleash my nerdy creativeness I fashioned several fictional races and types of ships they had. I once even managed to identify certain parts of a ship according to what section they belonged to. But never until now have I ever plotted out a ship specifically... much less construct one!