Well, it can be done... but is it advisable is the question.
The how is actually pretty simple. Let's use something simple like a Wordpress install. Say one homepage is "http://www.example.com" and the other is "http://www.another.com"
You could make http://www.example.com be the main site. The second homepage could be at "http://www.example.com/another". You can have http://www.another.com point to http://www.example.com/another, but still show www.another.com. Then you just configure the site with two overlapping domain names to the same site.
However... that's a silly approach. =p What I would recommend is you just have a landing page for the second one, which after that page points to the same site. Or, two separate sites.