Channel fly is more effective than manual heuristics such as 1/6/11. That's because it dynamically scores each channel it chooses based off ACTUAL throughout rather than predicted throughout.
In particular, sometimes overlapping channels with side interference will still outperform a busy non-overlapping channel. Or, you might be next to a very non-busy AP and even though Channelfly picked the same channel for both AP's, it's fine.
The key with Channelfly is that it's able to dynamically adapt to changing channel capacity. If you want to do a similar job, you basically need to run continuous surveys by hand!
