Well, having two types is no big deal, actually, they would have three, since the 742 and 744 fleet isn't common. After all, Atlas is an ACMI operator, so they have to buy what the customer needs, and as you know, not all customers need 747s.
Also, they are expanding, they are buying several 747-300's and converting them to freighters. They have also moved their headquarters to upstate NY, to be closer to their operations.
Atlas is a very well run, and conservative airline. They are one of the, if not THE biggest all cargo ACMI carrier.
Not sure of Cargolux.