Sorry yes you can also use the USB connection for MIDI IN per the manual. I have an 8x8 MIDI interface on my studio machine so I tend to forget about USB MIDI connections, with another benefit of a MIDI interface being that you'll reduce the chance for USB bus noise when connecting hardware that produces sound and transmits data and power over MIDI. But if you need MIDI IN and don't have a MIDI interface USB will indeed do fine.
The audio input on UNO units is a pass-through, I'd still recommend connecting each to their own channel(s) on your audio interface if you have the opportunity to.