Form follows function. Starfleet ships serve in multiple capacities but are usually designed around one primary function - combat, exploration, colonization, support, etc. Do you have a history for your ship/crew that leads in to your first story, or something your characters will refer to as happened to them prior to the story you're telling?
That aside, what Trek era is it -
early missing years (post ENT/pre TOS)
late missing years (post movies/pre TNG)
That will give you some basic design clues to what the ship parts look like, which in turn will start to dictate what the overall design should be.