Well heres how I do it...
I've got a cockpit tub prefabed with Nico's? pilot, everythings setup to resemble what a real cockpit would look like. The frame needs to be created on both sides (inside and outside), the glass however doesn't need to be created for the inside. If you want to do tweaking, not all sides of the frame need to be polyed, especially those that are never seen on the inside and very hard to see on the outside.
When your constructing the ship/cockpit tub you will definetely want to merge the two together to get the vertices to be exact, otherwise you'll see seams in-game and voids into space. Once their lined up, break the cockpit tub apart from the hull. In truespace I setup the cockpit internals, like cockpit, seat, pilot, HUD...etc as a subgroup, the glass and frame go with the hull. Otherwise I'd noticed when you look into a ship from the outside, the cockpit disappears.
Only other thing to do is setup the eye position. Which is quiet easy with truespace, (I just use an EngGlow point for that, convert to pof and notepad the "engine" position, delete it and use the cords for the eye.
:-)