Accessing the co-op optional missions are pretty straight forward with the exception of Chapter 11 & 14 (the final 2) which have specific triggers. Chapter 11 seems to only open right after the room where you previously destroyed the big drill. Chapter 14 the co-op door is unavailable until after you get both "Rosetta" parts from paleontology.
Its best to start and play the entire chapters on co-op from the beginning of them or in the case that you've already passed the sections of the chapter that triggers the co-op missions, just choose chapter select from the main menu and start the entire chapter over in co-op.
credit gamefaqs user Kagami84 for the tip