You can drag one deck into another and then that deck becomes a subdeck.  For textfugu, I first created an empty “Textfugu” deck and then two additional ones “Textfugu Vocab” and “Textfugu Sentences.”  Then I dragged those into the Textfugu deck.  After that, each time I import additional decks I just drag them into either vocab or sentences and that keeps them nice and organized the way I like them.  There’s a fair amount of flexibility in how you can do it, I think.