Complex sentence: Early Manhattan settlers sometimes found themselves in conflict with Native Americans and the town itself was threatened by pro-slavery Southerners, but the proximity of Fort Riley protected the settlement from the major violence visited upon other Free-State towns during the "Bleeding Kansas" era.
Split into simpler sentences: Early Manhattan settlers sometimes found themselves in conflict with Native Americans, and the town itself was threatened by pro-slavery Southerners. However, the proximity of Fort Riley protected the settlement from the major violence visited upon other Free-State towns during the "Bleeding Kansas" era.