There are often times when modeling with SketchUp that you have to resort to patching things up by hand. Patching things can be done quite easily with the Pencil tool.
There is only one rule for this: "Always stick to triangles."
When you select any three points in any space and then join them up, you always get a flat surface. When you draw lines defining a flat surface in SketchUp, it turns it into a face. Always draw triangles and you can't go wrong! Do not deviate from this rule to try to be clever, because you'll probably regret it.