I recommend building some lose open framework in creative mode. first figure out how long/wide you wand it, and then create some basic squared and rectangle sections out of the scaffold that you can easily delete later. after you have the general frame done, you can start putting some hull sections on, and start placing some giant system blocks "inside".
shields are based on the scale of the generator, so pick a number you want, 30k? 100k? 1 million? and scale up shield generators to give that output.
then, slap on a giant rock section to the bottom of the hold, and place your engines on the ship. (note, engines CAN be covered, and dont have to be fully visible). be sure to work the ship over to a nearby station, crew up and then see how the ship flies. Then with all these systems running, you can build your generator to be big enough to provide power for the other systems. be sure to leave excess power for system slots, etc.
oh, also once you figure out how it handles with the giant rock attached, remove it. its just to help account for the extra mass of the ships outer plating and decorations later...
so, once you play with systems and get something working, start filling in secondary things like cargo hold, or hanger bays, additional crew quarters, and then armor. once you filled in the gaps, start streamlining the outer hull and armor to match the design you want, and place decorations....
there uh.... does that help?