I'm currently running AES/EBU and RCA Digital into my DAC and RCA analog to my amp. The DAC has a remote control and all inputs are available so it's just a matter of switching inputs from the remote.
I'm not running any special digital cables. That being said I hear no differences when I switch between RCA Digital and AES/EBU. I want believe that AES/EBU is better but if someone switched the inputs I wouldn't be able to tell you which input was selected. That being said all the equipment is in the same rack. I suspect in cable runs over 20ft the AES/EBU would win.
The best method is try it and see if you can hear a difference. AES cables can be pretty cheap and tere are a lot of people who claim they can hear the difference. . For reference I'm using the PI2AES / Raspberry PI for a streamer and to me all the inputs sound good.