Complex sentence: Phelps believed that the property line would run through Seneca Lake to the west of the former Indian settlement at what is now present-day Geneva, which he planned to make the headquarters and location of the land sales office.
Split into simpler sentences: Phelps believed that the property line would run through Seneca Lake to the west of the former Indian settlement at what is now present-day Geneva. Phelps planned to make Geneva the headquarters and location of the land sales office.