Extra connector from p4304xxshcn front panel goes where on s1200v3rp board.
It's 2x2 pins in a 3x2 sized connector. The s1200v3rp board has 2 1x2 headers (J1F1 Chassis Intrusion Header and J1G2 HDD LED Header)
next to the larger front panel header J1C3.
As I understand, you are trying to connect the front panel connector and has question about it goes integrated. If I infer correctly, I'd recommend referring to
Connector Pin-out (J1E1):
You could find the Service Guide very useful, as well:
If you would still need further assistance, I'd appreciate if you could, please, provide more insight as to what extra connector that is you refer to.