One issue is that galaxies are 3D objects, so you'll need a 3D viewer/designer to make sense of everything. 2D views can be misleading, but perhaps no more misleading than 2D maps of planets' surfaces.Although spiral galaxies tend to be relatively thin, 1000 LY (a typical thickness) is a lot of room!
At any rate, you might want to consider using a 3D modeling program, although learning one might take more time than you're prepared to spend on the project. Personally, I found Anim8or easy to learn. It's free and runs under Windows. Blender is free, too, runs on Windows, MacOS and Linux, and is a lot more sophisticated.
FWIW, Orion's Arm has some maps that might provide some ideas.
http://www.orionsarm.com/eg-topic/49c787abb28fd
and there's at least one OA map being developed here:
Orions arm metaverse map



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Although spiral galaxies tend to be relatively thin, 1000 LY (a typical thickness) is a lot of room!

