Yes. In order for other channels to show up you have to add them in your Audio I/O setup which is unique per audio track. Once you add the additional channels, then you can assign audio to your sub-outs and aux channels.
In Studio One with a song open, click on
Studio One Options (Ctrl + , on PC or Apple Key + , on Mac)
Then select Song Setup
Then select Audio I/O Setup
There you have two tabs, one for input and one for output.
Add additional mono or stereo pairs and name them how you see fit by double clicking on the names.
Look in the Studio One manual for Audio I/O Setup for more information.