Let's start from the start...
WHAT KIND OF REMOTE ARE YOU USING?
Not all remotes are going to be able to do this. Harmony MAY have the Aton in its database, it may not, if it does not, then you will have to try something else, or more likely, you can call them.
Any remote that can work with CCF files (Pronto based) can have the codes from the Aton website loaded into it.
If you have some other 'cheapie' remote, then it may not accept the specific IR codes which Aton requires.
If Aton allows for the IR commands to be different than what they are expecting, it doesn't appear to be listed in their manual.
Instead what you should do is pick a zone - call zone 1 the kitchen, zone 2 the bedroom.
You will have a IR repeater in both the kitchen and the bedroom.
The kitchen IR repeater will be hooked to the Zone IR Inputs #1
The bedroom IR repeater will be hooked to the Zone IR Inputs #2
The remotes in use will use Aton IR codes (available at the link above, or in your Universal Remote programming section) and will perform the following commands:
1. Pick a source for the room you are in.
2. Adjust volume for the room you are in.
That's pretty close to it.
Additional controls (changing channel, presets, etc.) will be directed to the source output currently selected. So, if you pick source 3 (your cable box), then all subsequent commands from the remote control will be directed to the cable box which would be connected with an IR emitter to IR Emitter Outputs port #3.
But, it all starts with the remote control you are using and whether or not it is even capable of delivering the Aton IR codes which are required. (or do you have something specific that indicates that IR codes can be something other than what Aton has programmed them as?)