Complex sentence: These "Pimugnans" had settlements all over the island at one time or another, with their biggest villages, most likely, being at the Isthmus, and current day Avalon and Emerald Bay.
Split into simpler sentences: These "Pimugnans" had settlements all over the island at one time or another. Their biggest villages, most likely, were located at Avalon Bay, as well as at the Isthmus and Emerald Bay.