To answer my own question and maybe help someone who runs into the same thing.
Yes, Cube automagically creates everything you need in Mongo on the fly (db, collections, indexes, etc.). In fact, you should definitely let Cube do this, b/c when I tried to run that old schema-create.js script I had laying around, it evidently didn't create the proper indexes or collections or something, b/c none of my metrics collections were getting updated with new data, which resulted in terrible performance... unsurprisingly. So yeah... there you go. Let Cube do the Mongo work for you... don't try to do it yourself.