Yes,
If you use two rules now in the older version of Auto-Mate to file message received From and Sent to a contact, those two rules can be combined into one rule in version 3.0.
Just select Rule Type: Scan Messages after Receiving or Sending them
Then enter the contact in the combined From/To Field on the message properties tab.
It will perform the actions you choose when a message is Sent or Received from that contact.