First things first, some of this might be over my head so questions I ask are only for information not arguing and some info may need to be repeated

. In the panel at the house the grounds and neutrals are all connected to the same busses. 2 hot legs and one bare wire run down from the meter base, bare wire goes to the ground/neutral buss. I then have a separate ground wire that runs from the ground/netural buss to my water main that comes into the house. From what I see the grounds and neutrals are not separated from, each other.
Now to the sub panel. Are you saying that the grounds and neutrals do indeed need to be on separate busses in that panel and then running back to the main panel? What is the difference when they get to the main panel and essentially go to the same thing or do each of those wires not get hooked up to the ground/neutral buss that is in there? Also does the water line I have running out to the garage make any sort of difference or not? Thanks.