If sending an email and you want to track it against a CRm record, you will need to use the "Set Regarding" option on the CRM toolbar in Outlook. From there you will be able to select a record to associate with. Alternatively, if you have a record open, and from the ribbon use Add -> Email it will automatically set the Regarding field to that object.
You also have another option in Outlook with the CRM addon installed regarding email tracking. You can access these options in Outlook from File -> CRM -> Options -> Email Tab. There you can check the option to Check Incoming email and then set your preference below on which emails will automatically get tracked.
Previous emails will need to be tracked manually.