Is addon domain causing any SEO issue ?

I m on my new hosting account, which is using cPanel control panel, it’s been sometime since i last using cPanel, so i m trying to figure how to use it.

First thing i want to add an additional domain, going through the interface and i find out that i can add only add the new domain as addon domain, this raise my SEO alarm. Why ? When you add a addon domain on your main domain, it actually might create some duplicate content.

Let say  i have maindomain.com and seconddomain.com, so i going to add my seconddomain.com as addon domain for my maindomain.com , but after i done, i actually can access seconddomain.com by seconddomain.maindomain.com, it serve as subdomain. so the seconddomain.maindomain.com will actually have same content like seconddomain.com which will be getting penalized by search engine.

I digging around google for solution, which is something simple, just add .htaccess redirect from the subdomain to maindomain will do , sharing this with fiends that on share hosting and doing SEO.