I currently have two sites on two separate databases and installs under one domain, let's call it domain.com. One site is at domain.com and the other site is at domain.com/newsite. If this is possible, this is how I want everything to be setup, two sites, two databases and installs on one domain. Everything at domain.com works perfectly. If I go to domain.com/newsite the "Welcome to your new Drupal site" page appears as it should with a new empty site.
However, if I attempt to go to any of the admin pages under the second site domain.com/newsite/admin/*, I get a access denied page. If I log into my admin account for the first site at domain.com, I can then access the admin pages for the second site, however the admin pages appear to be using the content (content types, content, modules, blocks, themes, etc.) from the first site's database.
It appears that the admin sections for both sites are attempting to use the first site's database, as it relates to creating content, types, etc. For example, as long as you're logged in to domain.com, or have the correct permissions, going to domain.com/admin/* is the same as going to domain.com/newsite/admin/*. I don't know why specifically this is occurring, and if possible, I'd like to resolve this.