You don't enter the Connect Tone into the scanner. All that feature does is allow you to see the Connect Tone used by the system you are monitoring whe you go into analyze the control channel.
Like Mike said the system radio's use the Connect Tone to connect to the system. Kinda how radio's on analog conventional channels use PL or DPL codes to access repeaters. And the same with P25 conventional using NAC Network Access Codes to access P25 conventional repeaters.
I would say you shouldn't run into that problem since the scanner is getting that directly from the control channel data stream. But since the system you provided the link to into the database doesn't show a connect tone then I would say go with the one that the scanner is telling you it is.