If the generator is to be powering circuits through the main circuit panel, the earth/safety ground connection should be there, at the panel, and connecting to the generator chassis. So your generator hookup would need a ground, a neutral and one or two hots. (Two if split phase).
Generally electrical codes try to avoid multipoint grounding and the ground loops that result. Pity the same sound approach doesn't apply to the power co.
The safety issues of a transfer switch or other should be studied and considered.