Helpdesk can download messages only from one mailbox. If you’re using MultiSite Manager (MSM), you can set HelpDesk to download messages from a different mailbox on the other MSM site/s, however you can only configure and check one mailbox within one Helpdesk instance.
You can check multiple mailboxes though (e.g. sales@, support@) by creating various e-mail aliases on your main mailbox so that all relevant messages end up in one mailbox that can easily be checked from one Helpdesk instance.