The bluetooth remote only connects to one aTV at a time. So remote A will only control aTV A, and B with B.
you can unpair and re-pair the remotes, but for that you would need to unplug one of the aTVs, as the pairing process requires you to bring the remote within a few inches of the aTV.
the older IR remote (which also work with the new aTV), can be paired to work with a specific device.
(actually the remotes have an ID code from 0 to 254 and the receiver is told to only listen to a certain code, so you would have to pair each receiver with a different remote)
but...
the aTV supports multiple iTunes accounts.
you can have them both signed in, you just have to go to settings to change the account (it keeps the password)
your movie and TV store will change to reflect the chosen account.
the app store also changes, but the installed apps on your desktop ( TV top?? ) remain.
i'm not sure what happens to an app if you remove the associated itunes account.