Chaminda,
If you want to leverage TRNSHD with the TRNSYS3D SketchUp Plugin, you will need to model the PVs as windows (on each roof surface), as the shading insolation matrix is only applied to window surfaces. Also, the surrounding building objects need to be modeled as shading objects, as I don't think generic walls will be accounted for in the shading matrix calculations. Then you can specify a window material made of nothing so that irradiance passing through is not reduced by the window material. After that, you can have the irradiance passing through that window (representing your pv aperture), reduced by shading objects, as an output to compare against different configurations or to pass to an actual pv model (though this number would only be valid in a pv model if your pv panels have advanced power electronics to reduce partial shading losses). I hope that helps and is clear enough.
If anyone has a better way to do this, I'd be interested to know as well. I know there are specific components for inter-row pv shading calcs, but those don't account for nearby objects.
Best,
Luke