Motorcycle frame design starts with purchasing the parts that cannot be modified to fit the frame, like the engine, wheels, rider, etc. These are positioned over the frame building table in mid air using brackets. The frame is then built around these components. This method probably will work for a car.
You can do this virtually in 3D using computer aided design. The trick is finding or developing virtual parts like the engine, or in the case of a car, the engine, trans, rear end, steering gear, etc. You can save a lot of time if someone has modeled these shapes and you can use them.