Decide what the ship needs room for
Choose the ship's job first, then reserve room for the reactor, cargo, and any weapons the job calls for. The publisher's Main Sequence overview describes ships as modular builds, with cargo capacity, reactor placement, and armament left to the designer.
Lay out the equipment around the intended trip
A hauler needs enough room to take a useful load from one dock to another. Reserve the space you intend for cargo before adding optional sections. For a defense ship, plan space for its armament alongside the reactor and other equipment you need for the trip.
Keep an open section where you can test a different module arrangement later. If every part of the hull is already committed, even a small revision can force you to redo the parts around it.
Check the whole ship in use
Try the layout on the mission you built it for. If a hauler moves less cargo than you wanted, revisit how much of the hull you gave to storage. If a combat layout is awkward to revise, try shifting optional equipment before rebuilding the hull.
When the ship works, save the design for reuse. That gives you a reference if you decide to move the reactor or rethink the cargo area later.
FAQ
Does the reactor have to go next to a particular module?
The publisher describes reactor placement as a design decision. Check any placement constraints shown by your current editor for the specific part.
What should a cargo ship prioritize?
Start with the carrying capacity you need for the route, while keeping space for the reactor and other equipment required to make the trip.
Should I save every revision?
Save the versions you want to reuse or compare. A proven layout is especially useful as a baseline.