I have hosted my sites with Bluehost.com and the primary domain of the account let's say in this situation is maindomain.com
I bought another domain which we'll say newdomain.com and is linked with the hosting as an Addon domain.
Now here's my problem...............
Usually when you add an Addon domain in the cPanel it automatically creates a folder for it to upload the file. So the site can be accessed through maindomain.com/newdomain or newdomain.com.
In my bluehost's hosting package it also created a subdomain for it, for example we'll say newdomain.maindomain.com
So to avoid duplicate content issues I have added the following lines in the .htaccess file in the main directory of maindomain.com
Redirect 301 /newdomain/ http://www.newdomain.com/
Redirect 301 http://newdomain.maindomain.com/ http://www.newdomain.com/
When I search for site:maindomain.com in google I see it has indexed pages from maindomain.com/newdomain and newdomain.maindomain.com. And maindomain.com/newdomain redirects and works fine but the problem is the indexing. About newdomain.maindomain.com, just this URL redirects to newdomain.com and any other pages such as newdomain.maindomain.com/page1 never redirects.
Please help me in this to resolve this issue as soon as possible.