Eleanor used to prefer one side and had a flat head and now at nearly 10months old you wouldn't know she did have one.
We see a physio that was done through the child nurse. Maybe see if they can help you as the physio gave us lots of ideas on what to do.
Also try hold your little one with the flat bit not resting on you. Tummy time as well if he doesn't like it rest him on your tummy as they don't mind that as much or just across your arms or knees for a while.