In Calibre, if it is important to me, I list both the pen name and the author's name. For instance, Barbara Vine and Ruth Rendell are the same person. So all the Barbara Vine books are ALSO listed with Ruth Rendell as author. Nora Roberts also writes with the pen name J D Robb, but since I only read the J D Robb series with Eve Dallas, I just list it as J D Robb. Use an ampersand "&" to create folders for both author and pen name.
There was some brief discussion of this some years ago (search 'aliases'). That's where I found out how to use the ampersand.