Yes, you can.
You can let E-mail Converter monitor several folders automatically and direct the converted e-mails to different lists, like in the example on the screenshot below. Here E-mail Converter is set to do the following:
E-mails that are directed to the “HelpDesk” folder are converted into list items in the SharePoint-list “HelpDesk”
E-mails that are directed to the “Issue tracking” folder are converted into list items in the SharePoint-list “Internal”
