Hi there,
don't know if this is still relevant but here it goes.
When adding the e-mail account to your installation, the scanning service will take all e-mails from the "Inbox" folder and all e-mails that are not filtered with the settings in the 'Configuration\E-mail settings' page and import these.
They then either result in a reply being added to an existing ticket, or the creation of a new ticket.
The e-mail itself will be moved to the "Helpdesk_archive" folder. E-mails that are caught by the filters will be moved to the "Helpdesk_ignore" folder instead.
This should keep the "Inbox" folder empty.
The scanning service checks for new e-mails every couple of minutes.