Actually, you if you use Dr. Ralph's "Sprites," the program automatically creates a mask, as well as rendering your movie (or folder of picts) into a Nova compatable format.
As for making an animated sprite, let me make one clarification. If your ship takes 36 frames to rotate, you need to make one set of 36 (ship rotation) frames for each frame in the animation. For instance: I used an 8 frame walk cycle (would have used 16 for a smoother cycle, but Sprites couldn't handle that many frames) on my Gundam, and for each step in the cycle, I had to rotate the gundam once.
As for using alternating sprites, ATMOS put in the animated section in their base image (of the Thunderforge), except they made it pure black so it masked out the section of the ship where it would be. I'm assuming that the alternate is on a lower layer than the base, so if you render at an angle (45 degrees), using the black animated section in your base will mask out the base image so that the alternate image looks as if it's behind one part, but in front of another. Kinda on the same topic, I think that the engine glows and lights are on top of the base image, so if the base image is supposed to hide parts of the glows and lights, you need to render the ship (totally black, reflecting no light) as well as the glows.
Matrix
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Captain: What happen?
Mechanic: Someone set up us the bomb!
Operator: We get signal.
Captain: What!