I think I know what some of your problem is. You are using the mesh that shows as the squares. I always do the convert to switch it to the true polygons. The squares are actually 2 triangles, but the way it works is that they don't show.
Also with doing boolian functions, it can get real messy doing adds and subtracts if you do not clean up the vertices and extra polys that are sometimes created at the junction points. I always do this manually which can be somewhat time consuming, but it always gives the best results.
Here is a ship that I built using boolian and manual edits of vertices.
I actually have a little more work to do on the mesh and then comes the hard part of drawing the textures. Placing them on the model isn't that hard, but drawing nice ones can be a real pain.
BTW the model is 3616 polys and the smoothing is not turned on so all you see is the faceting. Once I reassign smooting areas it will be much nicer.