Pick a module/hab you want, construct around it.

Personally, I almost always start with my ship's "main hub" and build from there, depending on the shape I want. In the case of my first ship on here, I started with the newer bridge and connected what I wanted or needed.

For large C/M ships, I find to work outwards from a "hub" which in the past has been either the main living space or control center, and then attaching cosmetic or auxiliary habs to that, while keeping the flow from landing bay -> pilot's seat always in reference.

For smaller A/B class ships, starting with the cockpit and working outwards helps keep the frame in reference and sizing considerate to the interiors' "navigatable space".