Argh, too late!

Here's a trick I learned while making a Vaygr BC. (time is brief, daughter in tub, pictures later if possible)

Do a side view
Draw a set of panels lines
Use the lines to cut into the ship (boolean diff)
Do a one dimensional scale of the panel line chunk to shrink it into the middle of the ship
Use boolean union to join the main part and shrunk panel line section back together.