Open a command prompt in the folder you just created. For me this is C:\Program Files\Sun\SunSPOT\sdkblue080609
Connect a SPOT via USB and at a command prompt type "ant upgrade" and follow the prompts. You will usually be asked to reset the SPOT at some point. The upgrade also automatically applies itself to the eDemo board runtime.
This use of Ant always boggles my mind. I once spent an hour or so trying to understand how all the interwoven Ant stuff works here... and gave up. If anyone ever figures it out please post a link to the dissection in the TrackBot google group.
There is an additional step for the basestation - follow the directions on screen.