UOLT,
I'm not sure I understand your question. The engine should be centered on the thrust line. Whether the engine is mounted inverted or sideways, the thrustline won't change. Imagine the engine mounted inverted as per the plans. Now imagine holding the prop, and rotating the engine 90 degrees. That's the position you want it to be in. The top of the engine mount rails (Bottom of the mounting rails of the engine itself) are on the thrustline of the engine.