Complex sentence: It was shortly after that a rival Indian Tribe, the Appalousa (Opelousas) coming from the area between Atchalafaya River and Sabine River exterminated the Eastern Atakapa who occupied the area between Atchalafaya River and Bayou Nezpique (Attakapas Territory).
Split into simpler sentences: It was shortly after that a rival Indian tribe, the Appalousa (Opelousas), coming from the area between the Atchalafaya and Sabine Rivers, exterminated the Eastern Atakapa. They had occupied the area between Atchalafaya River and "Bayou Nezpique" (Attakapas Territory).