User's Guide: Add documentation on running CUPiD in a case

### What sort(s) of documentation issue is this?
- [x] Something is missing.

### What part(s) of the documentation does this concern?
- [x] [User's Guide](https://escomp.github.io/CTSM/users_guide/index.html) (using the model and related tools)

### Describe the issue

We need to add documentation on CUPiD to the User's Guide. Mostly this will be adding links to CUPiD/cime documentation.