Please refer to this KBA Designing FX3™/CX3-Based USB Type-C Products - KBA218460 for handling the CC line while designing FX3S based products with a Type C connector.
Note: There is a modification in the above KBA that will be updated soon. If you are using a Type C receptacle in your design, the AC coupling capacitors on the SuperSpeed TX lines should be placed between the MUX and the Type C receptacle.
Please let me know if more queries on this.
Perfect, thank you!