Having add-on domains does influence things from an SEO perspective as your add-on domain can be reached by different URL's.
Example:
Your main domain is shoes.co.uk on your hosting account.
Your newly created add-on domain is cars.co.uk
Your add-on domain can be reached by the following URL's.
Code:
1: cars.co.uk
2: cars.shoes.co.uk
3: shoes.co.uk/cars/
This means there are potential duplicate content issues when you're using add-on domains.
You could argue that if you don't link to 2 & 3 then you're in the clear and it won't be a problem then as Google doesn't know how to reach those URL's.
But what if you're competitor finds out about this?
Your competitor could start linking out to 2 & 3 and then your whole SEO position will be weakened because of the duplicate URL's.
Solution?
Use .htaccess code.
Open up Notepad and paste this code into it, of course you will need to change the example URL's to have it apply to your domains.
Code:
Options +FollowSymlinks
RewriteEngine On
RewriteCond %{HTTP_HOST} ^cars\.co.uk [NC]
RewriteRule ^(.*) http://www.cars.com/$1 [R=301,L]
RewriteCond %{HTTP_HOST} ^www\.cars\.shoes\.co.uk
RewriteRule ^(.*)$ http://www.cars.co.uk/$1 [R=permanent,L]
RewriteCond %{HTTP_HOST} ^cars\.shoes\.co.uk
RewriteRule ^(.*)$ http://www.cars.co.uk/$1 [R=permanent,L]
Save this as
.htaccess
Upload it to your add-on folder named
cars because that is your root directory for cars.co.uk
Also place a .htaccess file in the main root directory, thus in the root directory of shoes.co.uk that contains this code:
Code:
Options +FollowSymlinks
RewriteEngine on
Redirect /cars http://www.cars.co.uk
I'm not a coding expert, but this is working for me and it should work for you as well if you're using a Apache server.
I hope that helps a bit