On Peragus, C3 will be a party member and occupy slot No. 7 (Mira), but only for T3's mandatory run as PC. Beyond that, I think he's going to be either a temporary puppet or a character that the player can interact with.
If Nar Shaddaa wasn't so "sensitive", I would plug him in as a party member again in Vogga's warehouse. Unfortunately, I have found that the entire sequence of events from the meeting with Visquis through the boarding of Goto's yacht misfires badly if I mess around with the characters.