There is only one model, the confusion about there apparently being two models is because some model numbers end with A, some with B (it was also thought that the ones ending with B were the only ones that included the software upgrade pre-installed but that has been disproven).
The software upgrade can refer to two things: the January Software Upgrade which, for $20, you could install Mail, Maps, Stocks, Weather and Notes. The second is the upcoming 2.0 firmware, to be released on July 11, which will cost $9.95, and includes numerous updates, new features as well as the App Store. At the moment neither of these are available; the January upgrade was removed from iTunes as the five apps included within that will be available for a small fee from the App Store.