When using a different hostname for each company, the hostnames all simply need to point to the same document root.
So, if you have Blesta installed at /home/username/public_html/, then all hostnames for all companies need to point to this server path in your web server configuration. If you're using Apache, then in your httpd.conf, all the virtualhosts would have the same docroot. Please see http://docs.blesta.com/display/user/Creating+Companies#CreatingCompanies-ConfiguringCompanyHostnames for a sample configuration.
We highly suggest that if you are going to use multicompany that you install at a sub-domain. For example, billing.domain.com, account.domain.com, my.domain.com, etc. The reason is that you can have an actual website off domain.com as part of a different virtualhost. If you have Blesta installed in a sub-directory, and both domains have the same docroot, then they would also display the same website content.
I hope that helps!