The brake pad material on the rims is normal and you can clean it up occasionally with a green scotch pad. For your gears, cross chaining occurs on some setups if the gear ratio is too wide. Your doing the right thing when using the smallest ring on the crank, avoid using the highest gear on the cassette. And also when using the largest ring on the crank avoid using the lowest gear on the cassette. This will limit your crosschaining.