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@Eric Ringold's solution is correct. The intersect feature in the SketchUp plugin uses a native intersect feature of Sketchup that looks for adjacent and splits the surfaces. Then OpenStudio just uses the same observers that exist when you draw new surfaces to classify it as a base or sub-surface. Since a base surface can't be contained within another base surface it is classified as a sub-surface. If you forget to split the surface as Eric described, you can always split it after the fact and then erase and re-draw the sub-surface. This time it should be a base surface.

However, there is a much nicer solution now if you are willing to do surface matching in the OpenStudio application with a measure as described in this post. The native OpenStudio measure splits up the base surface for you.

@Eric Ringold's solution is correct. The intersect feature in the SketchUp plugin uses a native intersect feature of Sketchup that looks for adjacent and splits the surfaces. Then OpenStudio just uses the same observers that exist when you draw new surfaces to classify it as a base or sub-surface. Since a base surface can't be contained within another base surface it is classified as a sub-surface. If you forget to split the surface as Eric described, you can always split it after the fact and then erase and re-draw the sub-surface. This time it should be a base surface.

However, there is a much nicer solution now if you are willing to do surface matching in the OpenStudio application with a measure as described in this post. The native OpenStudio measure splits up the base surface for you.