VST Connect Pro doesn't send all sounds to the Performer

Reading this again…everything you want to send to the Performer from the Studio (Cubase/Nuendo) is transfered by feeding it to the VST Connect Cue send bus, regardless of the source. So in your case you would create audio tracks, one for each hardware input you want to send, set the source (input) of those audio tracks to your 1+2 Input Channel, and then enable monitor (white/yellow speaker button) on those channels - I assume you did all of this already so to hear your inputs? - and finally make sure that those audio tracks send to the VST Connect cue mix (enable rack/cues).
However I doubt that this will work, or if, there will probably be a long delay for the Performer, because realtime input cannot be used in a remote latency scenario as it is not in sync with the delayed Studio playback.