In a situation where you have an existing website and wish to retain the homepage, the best option is to install ClassiPress in a subdirectory. ClassiPress requires its own instance of WordPress to run, so you would install it something like this:
yoursite.com <=== Your current homepage
yoursite.com/classifieds <=== Your ClassiPress installation
You could simply use the WordPress custom menus feature to create links between the different parts of your site.
Then in terms of sharing the user database you can find many online tutorials if you search Google, such as
this. So that your customers only need one login for the entire site.
