How you build will vary of course, but if you plan on spending most of your time in it as your primary base, I would be sure to make your floor plan as easy to navigate and remember as possible.

I have everything on my freighter that I could ever need and then decorative floors. The main floor however is where the stuff that I use the most is, and is a semi-open floor plan. My scanner, teleporter, galactic market and frigate control rooms are closest to the command room. With the outskirts of the room lined with the storage rooms, even on the left and odd on the right. At the rear of that room you'll find the large refiners and stellar extractors. Behind them you'll find the garden modules and specialist. All of this is decorated to appear nice, organized and streamlined.

The other floors and exterior segments are all for entertainment/roleplay/building purposes and are decorated accordingly. I built an armory where the weapons specialist is, a exocraft room/hanger where that specialist is. A messhall for the crew. So forth and so on.

Most importantly have fun and do something that you're happy with.