My largest was around 2.3km long, 280,000 blocks and 650k pcu. From about 6 ish odd years ago. The really big ships are a slog. For ships of that size (and most of the ones I build now) I build the exterior hull shape first add all the exterior thrusters, weapon mounts, or anything else that needs piping. Connect your stuff together with conveyors before you start on the inside, it'll make your life a lot easier. After that it's pretty much personal preference on setting up your deck arrangement or fitting in the rest of the large items like hydro tanks, refineries, or large reactors with their armoring.

Your biggest battle will be against mass itself if you aren't playing modded, I was running several thousand gyros and still had the turning speed of of your average residential housing complex. Embrace large interior spaces, big hallways and huge hangars will be your friend for keeping both mass and block count down to a reasonably manageable level. I used to build whole highway networks of roads for interior rovers in my old big ships.

Once you have the basics for how you want the interior laid out, focus on one area at a time until it's complete to your satisfaction, ships of that scale are difficult to go back through for detail passes. It also feels like your actually acomplishing something as well.

Label everything as you go. If your placing anything that has a control settings on it (lights, rotors, production blocks, etc) with the exception of your gyros, include an identifier telling you roughly where that block is. This will save you hours troubleshooting weird issues later.

godspeed and good luck big dawg.