How to organize/sort alias mails?
Is doesn’t matter if you use a mail sorting rule (found in Mail’s preferences) to move the mail to the target mailbox of your choice or if you create a smart mailbox to display the mail which will keep staying inside the inbox. All you need is a rule of this type:

Any recipient is aliasname@maildomain.com


This should separate your mails to different mailboxes as you described.