Controlling multiple Apple TVs

I’m looking for a solution to control three Apple TVs that are next to each other. Right now I’ve set it up by having three universal remotes broadcast random signals obtained from other devices that are taught to the Apple TVs. I’ve thought of two ways I can use Roomie to control them:

Pair each of the original Apple TV remotes back to each Apple TV. My understanding is if they are individually paired, they won't interfere with each other. Then teach each individual remote to Roomie. I'm unsure of how the "pairing" works (does it change to unique IR codes?), so I don't know if this will work.
Teach Roomie the codes from the universal remotes I was using.

Method 2 should obviously work, but I wanted to check if 1 was possible only to make future troubleshooting/reconfiguration easier.

Learning 3 paired custom command sets would be one technique that might work. Using discrete emitters, one emitter per AppleTV, with emitter shields would probably be more reliable in the long run. Some emitters with shields are shown here: … TF8&node=9