I think I can help you finding a solution… If I understand you good you want to have control by the input faders (not the gain which is controlled by hardware) and your outputs in your Cubase… anyway probably this will gonna help you…
Try to set your Focusrite Mixer in the routing on “mixing” preset if you have (I have Liquid 56 and there is)… if you don’t, then set in the routing section DAW 1-2 to Main Mix, Daw 3-4 to Output 3-4 or whatever you are using and how many you have connected… In the mixer/fader section set DAW 1-2 to ASIO OUT. On ther main mixer output of the mixer/fader section do not set nothing… unnattach whatever you have there…
You can also mute all the channels in Focusrite Mixer to be sure you are not duubling signal.
Now, open Cubase and try to connect anything how you wanted or do even better and my advice for you is to get to know with Control Room feature in Cubase… it’s really nice and it could be usefull tool for you…
here is a link to a post about how to work with CR…
…in the beggining of the post you have a links to a youtube lessons which are made very easily to understand.
I hope it’ll help…