I have never done it, but the theory is simple.
If you look on the pirate base, you can see a rotating pirate head. Now, imagine if that head was say....a cool turret. You'd have a rotating turret! (no garentees that it actully fires properly though)
So, what you do is, make the ship in softimage XSI (model, UV, texture..ext) (Wings3D is good too)
Leave OUT the part that you want to animate, model, UV and texture that part SEPERATLY.
Then, when you apply Null points to your ship, put one where you want your animated part to go.
Then, make a particle effect, with your model of the part, so that the part rotates (or whatever) the way you want it too.
If you have named everything correctly, and made everything correctly, that theorectly should give you an animated part.
However, the part cannot track or do any complicated movments. Rotation is about the best you can do.
NOTE: I am very weak on the moddeling/texturing part. If you want more help, find the seven deadly sins site, and go to there wiki, they have a couple good tutorials thier. Though, I've never understood them well enough to do it myself..