In putting in a 100 amp sub panel using 6/3 wire I have wired it to sub panel but an woundering about the main do I have to put both the ground and the neutral on the same bus? Or make an

Your sentence is incomplete so we don't know what you are asking after... or make an? What is the AMP rating of the main box? 6/3 is only rated for 50 Amps, not 100