What's gonna happen is that certain faces (the red outlines) will be layered over others. Best bet is to go through and seperate these faces. For instance, it looks like your cannons on those pods will have their UV map space layered over the space for the side of the nose. Find these and pull them away.
Next step is to find all mirror images, and I mean all! Flip them and arrange them over one another, so that you only need to texture one side and it corrosponds to the opposite. Not only does this speed up texturing but it also allows for better looking textures.
Third, spend a few minutes arranging all your new groups in a very tight perfect square. After you have done this increase their scale so that they completely fill the UV map space. AHAH! You are done! Well, after you save the map that is.
Have fun! (And after come texture my models, because I am just plain horrible at 2d art.)
~Beowulf
Edit: What exactly is this "Lithium Unwrap" of which you speak?
