Hi Vince,

What you're seeing is most likely coming from the geometry. You almost always want to make sure that your models are made of either quads (4 edges) or tris (3 edges). ngons (more than 4 edges) can cause issues with normals, uv mapping, beveling and so on. So I would recommend going in and fixing up some of the geometry.

In regards to the texture area, you can work outside of the 0-1 texture space (the top right corner), but it's not very common. If you run out of space, simply scale down what you have, and put more stuff in there. You can bake that area into whatever texture size you wish, so it doesn't really matter how large each shell is.

Regarding your planar mapping tool, try opening up the option box and resetting it.

Tip: Try automatic mapping the entire object at once. Since your model is cube-like, automatic mapping will give you a good start.