No. the retail version comes with the software. The education version does not come w/ the software b/c it assumes schools would be buying a site license.

I can't recall about the storage bin...i got a tackle box which fits all the components nicely. In the top part, fits the balls, wheels, NXT brick, cables. Beneath that, are 4 of those tackle boxes where you put in the moveable dividers. All the rest of the parts are sorted by type in those bins.