Hi , you can run any number of drupal sites on one core files and folders ... I run 12 drupal sites only used one drupal core files . drupal 7 : Your main domain : site.com You want will be install domain.com website on sites.com core files : you need to create a folder on site.com root path : sites/domain.com copy default.setting.php file on /sites/default folder to /sites/domain.com/ and rename it to setting.php you need to point domain.com via dns or virtual host to site.com The end , you now can install domain.com website ....
You can also use aegir which uses the same drupal multisite concept I see it as a multi-site management tool across multiple drupal installations at its core but can extend into a lot more. It has functions to deploy and backups sites, You can also work with different drupal versions using platforms. You should give it a try it will make your management easier