I don't like automappers that much myself. Especially uvunwrap using an entire section... too many polys.
What I do is take sections like wings, pods, base hull, detail hull parts, etc... if possible use UVmap planar.
Make sure you set the width/height sizes equal to make the map porportionally correct rather than just use fit.
Then run the UV unwrap to adjust it to your liking.
Rescale it to match what you've already done.
Move it to an area outside the normal (0,0)-(1,1). Once you've got all the pieces mapped.
Select everything and rearrange the parts so that they start at (0,0) but don't rescale them down just yet.
Once they're all in a nice big block then rescale them down to (0,0)-(1,1).