As Felix indicates the use of multiple virtual apple remotes steered with a Harmony remote is not supported but it nevertheless works like a charm for me. I can toggle fullscreen, record/play etc on any button of my Harmony remote and thus address all functions the regular EyeTV remote allows (and more). 
If you are interested in this, please look at the thread "Harmony 555, IR receiver and RB/Plex/EyeTV" in this forum.

However, it does not solve your question to alter the buttons when inside the EyeTV menu, as Felix indicates. I also have not found a way to open specific EyeTV menu items (calling the EPG for instance while inside the live window) with a single buttonpush if they are not available in the normal EyeTV buttonbar at the top of my desktop or as an action in Remote Buddy. 
Actions you can call with a keystroke however are easily programmed in Remote Buddy (e.g. close/open live window etc)