I'm not entirely sure I know what the problem is but here goes...
While in Cubase
Press F4 on your keyboard, it should open up "VST Connections"
Alternatively: Click on "Devices - Vst Connections"
Click on "Inputs" tab, and then click on "Add Bus", select the number of inputs your soundcard has, then choose Stereo or Mono - if it's inputs for microphones or guitars, I suggest choosing Mono - easier to manage in cubase mixer.
Cubase should pick up your soundcards inputs and put them in the busses automatically.
If not, then you can choose the inputs on each bus, by clicking on "Device Port"
Here's an image with highlights.
I hope I understood your problem correctly, and that this helps you. :)