The Aquanotes software from what I've seen so far is complete database program to keep track of everything going on with the tank, not just what the ACIIIPro's probes and control program are doing.
Since its tax season think of it like this: Aquanotes is like Quickbooks and the ACIIIPro is like TurboTax. Wait, does that make sense? I hope so. If you want to "LOG" everything then get the Aquanotes software. If you want to monitor and control but dont really care to much for graphing or logging over a long time period then you could probably pass on the software.