What you want to do is perfectly possible in Cubase.
Things to check:-
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Your microphones are connected to two different mono physical inputs on your audio interface.
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In VST Connections Inputs your “mono 1” and “mono 2” buses are connected respectively to the two different mono outputs from the audio interface (the ones corresponding to the physical inputs your microphones are connected to).
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On the inspector for the mono audio tracks, the “track 1” input should be set to “mono 1” and the “track 2” input to “mono 2”.
If the connections are now correct, when you record arm both tracks and hit record on the transport you should be able to capture each mic separately on its respective track.