wow i was in a shop and i went to see what a certain part did and when i exited my whole ship was back to just the core and i didn't move anything off or on my ship.
masta ali when you put the part in its place, there should be a box above it ,click it and hold it ,then move your mouse in the direction you want to rotate the item.
http://img195.imageshack.us/img195/3867/scr6c771d.jpg thats what my ship looks like so far ... i can stay in a dead zone long enough to kill the enemy ship and then i have to get out