BP main site with regular blogs subdomain custom menu error


I have setup BuddyPress as the main site, but want to link a blog as a sub-domain to each group. When I am setting up a sub-domain site and go in to use custom menus, it redirects me back to the main BuddyPress site. On the dashboard of the sub-domain site I also see the comments from the main BP site. What is causing this and how can I correct? I do not want BP on all sites, just the main site, but I want all sub-domain admin sites to be independent and just pull in blog posts to the group. I am sure it is something in the settings, but somehow I am missing it.