Modeling isn't brain surgery. But, if you haven't done it then it's confusing. Once you get in there and figure out how it works, you'll go, "oh, I see" and you'll never look back. For clean modeling you can't have any holes or vertices that are not attached to anything. If two verts are on top of each other, they need to be welded into one vertex. If you have a hole, you need to fill it in with a plane. I think you have it now.