Under separate cover is a phrase used in letters (or emails, though less so) to indicate that additional material has been sent separately from the initial message. Usage of the term indicates that there is more to follow, usually something of a different nature than the initial letter - contracts, photographs, ransom notes, etc. The phrase is used less nowadays than it once was, either because (I'm guessing, here) more messages are sent through a variety of communications channels and the phrase rather explicitly refers to actual, physical mail, or because it sounds, well, stodgy.
Me, I like the sound of it. Feels charming, in a businessy sort of way.