Hello
@ainzz and Welcome!
I can hopefully answer some of your questions, I'm sure more will chime in.
Make sure when using USB you are using the Bottom USB port, The top one is for connecting a hard drive or other file source. I don't see any reason why it shouldn't recognize your RME, if anything I would do a reset with the RME connected to the proper port from within the ifi app or ifi.local, when you do this make sure nothing is connected to the Spdif.
If I remember correctly the way the ZS is setup is that only one of the outputs can be used, and one disables the other. (trying to answer your concerns, would have to look it up to be crystal)
In terms of sound quality I think you are going to be very pleased, "Carbon" or no "Carbon at the moment, as the Zen has bested just about everything we have tried in this thread.
Both outputs of the ZS are very good, and it will be down to what the DAC prefers in my opinion as to which sounds better. Just as an example My Schiit Bifrost 2 prefers the USB of the ZEN, Spdif sounds very good but the nature of the DAC is that USB Sounds better, follow the thinking??
My Gustard X16 sounds better using the Spdif from the Zen vs the USB like the BF2 so experiment around and see what you and your DAC prefer.
Hope that helps sort things out for you, and feel free to ask anything, and also please give your opinion when you've settled in on everything.
Cheers!!