Yes, you can go ahead and do the v6 software upgrade.  I say this from experience of doing the upgrade (a couple of times, since I was in the beta test group), then purchasing a SkyRadar and finding it didn't work, then doing the OS upgrade, then (eventually) seeing the SkyRadar work.
EDIT:  I must retract my statement about having the SkyRadar work.  I'm still having some issues; however, I seriously doubt they have anything to do with the order in which the OS update and v6 software were installed.