Multisites can have their own unique aliases called site aliases which you set in the folder properties of the multisite folder. In 9.0 SP2 (with no cu's applied) there is an issue where aliases used on content within a multisite will not work when used with the site alias. For example, if your site alias is 'www.multisitealias.com' and a content alias within that multisite is '/content_alias/' then the URL 'www.multisitealias.com/content_alias/' would give a page not found error.
Apply the site update for 9.0 SP2 available at /downloads/. Be sure to backup your database and site files beforehand. For site aliases to work you also need a binding on the site in IIS and a DNS or host file mapping. Please refer to the product documentation on how this is configured.