Rowmote determines what it is controlling by the name of the Mac or Apple TV. However, the Apple TV has the name ‘AppleTV’ by default, so multiple Apple TVs show up as a single item.
You need to change the name of each device to be unique so that Rowmote can see them separately.
AppleTV 2 (Black)
Simply change the name of the AppleTV via the Settings on the device. That's it. You may need to restart the AppleTV by removing and then reinserting its power plug for the change to be visible in Rowmote.
AppleTV 1 (Silver)
Changing the name is a little more complicated than with the AppleTV 2. You need to use ssh (from Terminal: /Applications/Utilities/Terminal.app) and issue two commands.
Password: frontrow
sudo scutil –set LocalHostName new_name
sudo scutil –set ComputerName new_name
Where new_name is a name for the AppleTV. For example:
sudo scutil –set LocalHostName "Living Room ATV"
sudo scutil –set ComputerName "Living Room ATV"
To do this for each AppleTV, unplug all but one, issue the commands, then unplug and replug in that one. Then repeat the process for each of the others.