Connecting a device to a CPU via USB PCB tracks
Is there any problem in the above way of connecting the two devices?
  What type of consideration do I need to take of? 
  Can I do just connect the wires to each other, or do I need some type of     interface? 
  Do I need all the normal surge/over voltage and ... on this design? 
  Is there any sample schematic that I can use as reference?
  


My answers:

1: No, there is no problem in connecting two USB devices (a device to a host) on the same board. It is called "embedded USB".

2 and 3:  You need to provide trace layout that conforms to USB3 signal integrity requirements, just straight connection, Rx to Tx, Tx to Rx, with AC decopling caps, all as a normal USB connector will provide.

4: No, you don't need any "normal" surge/overvoltage etc. protection, since the link is embedded, and there is nothing to protect it against.

5: It might be difficult to find. All laptop docking stations should be using embedded chips, including Super-Speed chips. In general, look for USB 3.0 design guides, similar to this one, or TI guide. 

ADDITION: I would advise to arrange for some power sequencing between the SoC and FX3, to force the FX3 to come up after the SoC gets ready. It can be done via power gating, or keeping the FX3 in reset using some GPIO. It would help to avoid accidents when FX3 side would go into "compliance mode" (test mode) if SoC starts with SS termination but wouldn't be ready to respond to LFPS handshake in time. It is better be safe than sorry.