Once you place the origin (cube) its sides determine the orientation of the ship. The best way to keep track of the ship orientation is to immediately attach two dummy parts to the cube (and give them an offset away from the cube). This allows you to see which way is which.
And because of the hex grid map, any wobble during flight is to be expected, but its stem should always be (roughly) pointing toward the destination. If you fly by hand (eg manually 1 tile at a time) the ship should rotate toward the destination tile, but should fly nose first.
