From your report i get that having 300 arms , 300 horses on the colony and a galleon with the same is optimal defense strategy
Playing 0.11.6. on very hard I used to have many issues with native, then i restarted and tested this strategy: put cities away from native land whnever possible, and never buy/take native land Missionaries on every capital and on native settlements too close too you. Be ready to displace other countries missionaires at the key places if you take an european city deep side native land, be ready to vacate the land ASAP keep an eye out for any settement that is not happy, and send missinaires and gifts...