You may be missing the point of Live Paint then. Build your "Live Paint" object using single lines that are tangent or overlapping. When converted to "Live Paint" each area and line can be individually colorized. Moving one line (with the Direct Selection tool) will change all shapes associated with that line.
When "Expanded" these shapes will be converted to closed shapes. By starting with two lines instead of one, AI may be creating unnecessary shapes between your intended shapes.