Hello Kent,
Are you using MSD or HID components on Processor Expert? If so, then PEx configures all (USB clock and USB stack configuration) and you do not need to add anything else (if autoinitialization is enabled, otherwise, you will need to con USB_Class_xxx_init function).
If you only add fsl_usb_framework, then, you need to configure USB module manually.
You can give a look to this document for USB device: Creating a New USB project with KSDK and Processor Expert support in KDS (It was created for KSDK 1.2 but same principle applies for 1.3) or here is another document for USB Host: https://community.nxp.com/docs/DOC-331376.
I hope this can help you!
Regards,
Isaac