Generally speaking, ChannelFly (or in standalone lingo, "SmartSelect") will select the optimal channels for your area, particularly in a crowded RF environment with lots of rogue AP's. Furthermore, ChannelFly responds *dynamically* in realtime to changes in the RF spectrum. For example, channel 1 might be unused in your house, but let's say you invite me to dinner and I'm a jerk -- I could take out my cell phone and tether it to my laptop using wifi channel 1, and all of sudden channel 1 is hogged by me. If you were using ChannelFly, within a few seconds your AP would realize channel 1 now has very little capacity compared to before, and switch to a different channel.
So that's the good news... The bad news is: ChannelFly attempts to announce / coordinate its channel changes through a protocol called 802.11h, which allows an AP to alert clients that a channel change is about to happen. Clients are supposed to heed that advisory and hence seamlessly migrate to the new channel. However, not all clients gracefully handle these advisories. Sometimes, when ChannelFly changes channels, it causes a poorly behaving client to just lose the wifi network.
If you have such poorly behaving clients, you can try to increase the ChannelFly MTBC (Mean Time Between Change) such that switches become less frequent. Or, some folks like a "run stop" mode of operation, where you run ChannelFly for a few hours to see what channels the AP's pick automatically, then you manually lock the AP's on those channels. That, however, loses the benefit of ChannelFly's ability to adapt in realtime to changes in nearby rogue AP traffic.
If your home RF environment is relatively clean, then you might benefit from static channel assignment. However, I live in a dense apartment complex and see 100+ rogue AP's. For me, ChannelFly's ability to find the cleanest channel is well worth the tradeoff of occasional channel changes (e.g. once every 4 hours), especially since the majority of my devices are also Apple devices and they seem to handle the channel changes gracefully.