There is a feature in EDACS, called ProScan, which will allow the radio to roam in between multiple EDACS sites seamlessly. This option does cost money, so this may be the reason that your agency has chosen to have the users switch between sites manually. I believe that there is an option in the radio that will allow the radio to sound a tone when sites switch, but I think that it can be turned off. It's been a while since I have been in ProGrammer...
Yes, "CC SCAN" indicates that the radio is out of range of a control channel and is actively scanning the programmed list of control channel frequencies for the presence of a control channel.
I really am surprised that they are making you manually switch sites. Personally, i'd question whether the programming is correct or not - but I don't know if your position will allow for such questioning. :\