What I usually do is draw something on paper first, or make a smallish scale ship. Then I set what I want for shields, thrust etc. and the amount of turrets I want. Then I build. core location is very important in this, a core in a conning tower looks nice but will be easily shot off in a fire-fight. Putting the core deep inside the ship is usually the best option, just make it accesible.
Next, shapes.
Think, what do you want it to have a feel of? a borg cube? a star destroyer? some other design? usually I pick a ship already from a series or movie jsut to giver me an idea. Often the child ship looks radically different but that is what you want. Look for guides on waht diameter you should have for cylinders or spheres. and of course, try it out.
next, internal systems
so an easy thing to do is to pile a huge amount of shields, power blocks, etc. intead, try reactors, or at least make lines or L\'s instead, they are much more efficient and allowmore crap to be shoved between them. always add good power and shields if anything at all. Also, don\'t maje bigger and bigger guns, jsut make several small guns that do 300 damage each. missle should only be used at the end when the shields go down. go for largre missle setups, sd-bb is the best ofr all sizes and sd-kb is best for fighters and turret less corvettes.
next, docked turrets and drones
so now that you have a hull and internal systems, turrets and hangars may be what you look at next. turrets are great in large sizes, not so much in the smaller sizes. you should have them do between 200 and 300 damage per shot, then add more barrels to them. make minor power systems to support shield regen, but no need to make a power system for the guns, they draw power from the ship itself. a few heavy or medium turrets are better than a bunch of small ones, and are better at reducing lag on servers. drones are small and are best used on carriers with a rear facing door. that way you can drop and run for the win
hope this all helps
