There are two ways you can do this.
1- Alt sprite frames like the Thunderforge- spin your sprite as normal, but black mask out where you want the spinning object (this means substitute a black, nonspinning placeholder in your model where the rotating part will be). Spin it to rle- this is your base sprite. Then, make another rle where the base sprite is the black mask and the rotating part is visible. Spin one revolution of the sprite, index your rotating part, spin again. Repeat this process as often as you need to get a smooth rotation. The black masks here make it so the part that is rotating is neither covering up nor being covered up by another part of the ship.
2- The Leviathan simply a basesetcount of 3, where each set had the cargo pods rotating slightly. It took 3 seperate spins of the sprite to make a smooth animation. This process is much like setting up a sprite to bank..